How long could this system last after Napoleon dies? Who takes over after him? How would it affect Europe's development, particularly in so far as liberal ideas were counter-cultural for much of the 19th Century, but here they would be hegemonic from the start?
What kind of republics are we talking about here? Because Napoleon's France, even in its republican phase, is very much a dictatorship. By 1804, Napoleon has already made himself a consul for life, and is an absolute monarch in all sense, but the title. He is also the president of the Italian republic, though I believe only for a 10 year term there. And if he lasts in these positions untill his death, how much does it change the ideas of republicanism in Europe? After all, Napoleon has shown that the style of leadership of a republic can be quite the same, as that of the Absolute monarchies of Europe. One can even be the ""democratic leader"" of several countries at once.
Meanwhile his conquests seem problematic to survive long-term.
A Rhenish Republic to protect France's western flank.
The Rhine territories were considered to be an integral parts of the newly forged French republic. Unless this means some kind of Country EAST of the Rhine, as a French buffer, it would make little sense for Napoleon to give up this territory, and would cause much anger in France (as late as the deffense of homeland campaign, Napoleon was insisting on preserving the Rhine border). It would however likely be the country, where Republicanism in French form (either napoleonic or more liberal), could actually last. The other three...
- A Polish Republic to check Prussia, Austria, and Russia.
- An Hungarian Republic to further check Austria.
If there was one fact in both of these country, it was the strenght of the local nobility, that would in some form last up untill World war 2. The nobles own almost all the land, they benefit from the allegiance of the mostly uneducated commoners, and enjoy the support of the Church. This was something even Napoleon and Davout (who had rather dim view of the Polish nobility during his local tenure, aside from Poniatowski), had to recognize, and act cautiously with.
Now, a Republican form of government isn't completely impossible here, but it would very much be Aristocratc republics. Which is extremely distant from the ideas of the French revolution, though considering Napoleon's role as autocrat, it wouldn't be that surprising. There are now presidents in Hungary and Poland, almost certainly nobles, elected by nobles. Does that seem like a liberal system?
Or Napoleon could go full-on revolution. All power to the people, seize the lands of the nobility, a bit of state terror to liquidate those pesky aristocrats. Expect, he would be extremely hard pressed to find anyone else to put in power. A few eduacated traders and city dwellers could be found, but would have little to-no experience running anything like a country. He is also likely to face a hostile church, who has an extremely high influence in both Poland and Hungary, and will be terrified by the possibility of loosing their rights and wealth.
He could force French officials to handle these things, which would show him as a foreign invader, forcing a regime and foreigners on these countries (which he was).
By the time of Napoleon's death, these Eastern allies will either be a) somewhat stable republics in name only, controlled by the local aristocracy, who might well decide to invite a new king, as long as he keeps their priviliges b) barely functioning republics, with only somewhat experienced administrators, possibly facing food shortages due to rushed and radical land seizing policies, with a lot of exiled nobles in Vienna, Berlin and Petrograd, beging the old monarchs to come and restore order c) almost completely disfunctional French protectorates, utterly hated by their populations.
In all of these cases, they will be surrounded by hostile powers, hoping to carve them to pieces. More on that later.
The kingdoms of Spain and Portugal dissolved, and replaced by several sister republics (Algarves, Lusitania, Galicia, Castille, Aragon, and Navarre).
Option c from the previous part is very much active here. A series of artificial states, despised by the conservative locals, run by a country that has previously acted harshly against the holy church? Even if Napoleon manages to completely crush the local guerrilas, and beat any uprising that springs up, the moment that he dies, the whole collection of monstrosities is going to come crushing down.
The next big problem is Napoleon himslef. Or rather the fact of what happens after his death. There will be a highly powerfull millitary, probably rather fine with a dictatorial republic. The parlamentariens will likely want more powers. Napoleons relatives and in-laws will want to keep their powers and leadership positions. There are still regions like Vendee with strong Bourbon sympathies. Its a powderkeg waiting to explode, and tear the whole country apart.
The foreing situation is even worse. Britain will almost certainly support the Spanish Bourbons (could have very interesting effect on Americas) and Braganzas, as a French hegemony over Spain is utterly unacceptable. In Russia, Alexander will have to tolerate not only an independant Polish state, but a republican Polish state, and unless Russia is extremely unlucky and gets a tsar Constantine, any ruler of it will likely see to wipe a Polish state off the map. Habsburgs will still have their core territories in Austria, Bohemia and perhaps Croatia under control, and will certainly want a full revenge, to say nothing of Prussian desire to reclaim Poznan and expand in the West. The other German states will either be under French dominance or somewhat independant, mostly monarchies, and likely terrified of France spreading revolution to them, while nationalistic outrage over French Rhineland will also be quite problematic. So basically, everyone not under him wants Napoleon's creation dead, and is only kept at bay out of fear of Napoleon, and French strenght, something highly likely to end with Napoleon's death.
I expect a rather interesting inpact on Nationalism. In Germany, with Napoleon holding the Rhine provinces (either directly or as a puppet state), an extremely anti-French version of it is likely to develop. Liberation of the Rhine is going to be the main goal alongside unity itself. Meanwhile, Austria might actually take a strongly nationalist turn. This actually occured under von Stadion during the 5. coalition, where the Austrians experimented with supporting anti-French nationalists (for example: Archduke Karl's call for a German uprising upon his entry into Bavaria, support for the Tyrolean rebels, and the nationalist fervour that was encouraged among the common people to great success), and with such a reduced state of the empire, this outlook might take center stage.
In Spain, which was torn apart by the French, it is not a even a question, the local nationalism is going to be extremely anti-French, with a very similar situation likely arising in Portugal. Meanwhile, Italian nationalists are also not likely to be too pro-French. Napoleon might have declared an Italian republic, but it is effectively a French puppet, that only controls the North of the peninsula, and not even all of it. Let's not even get into all the problems with the papacy. The repulic in Naples, judging by the quick collapse of the Parthenopean Republic the moment the French troops withdrew in 1799, is likely to be kept alive by French bayonets, with local elites support, while king Ferdinand is waiting at Sicily, with British support. I wouldn't be too surprised, if Italian nationalists took the view thta Napoleon was just another foreign overlord, who forced himself as Italian head of state.
Even in the "liberated" Poland and Hungary, nationalism is going to be rather confused. After all, the independant states are either run by the nobility, or by the French. Neither fits very well with ideas of liberalism, and the rather is quite anti-nationalistic.
Honestly, I expect the effect on liberalism and republicanism to be rather negative. In France, the republic has been subverted to be a one-man Autocracy. In other countries, the local republics are either noble-controlled, kept alive by French arms, or utterly hated by the local populace, with a few expections like Switzerland. That is not a good look for Republicanism, especially if the power struggle after Napoleon's death results in some form of civil war.