This would have happened too late to butterfly away the existence of Augusto Sandino, who could have made trips through the canal very… exciting… while he was in business.
Not exactly, Sandino wasn't revolutionized until the US intervention in 1912, which would be butterflied away by the building of a Nicaragua Canal. Who knows where he would end up with a POD in 1902.
How the US decides on Nicaragua would have some interesting consequences -
If it happens because T. Roosevelt is not president, that is one thing. If it happens because the Congress pushes forward the Nicaragua idea against Roosevelt's wishes, then we have an interesting political blow to him that would have consequences. It could be that without the American intervention Roosevelt actually is in a stronger political standing, with the isolationists less upset.
Panama would remain part of Colombia unless the US decides to intervene at some other point. It may push all of Colombia over the edge, with the country torn apart over what to do about their rebellious territory to the north.
If Colombia ends up at war with any of its neighbors, supporting the Panamanian rebels would certainly be a good strategy.
IIRC the Nicaragua Canal was in the south of the country and relatively close to Costa Rica. US affairs would therefore be much more interested in that country as well as Nicaragua.
Other than that I cannot really think of any big differences. Any eruption of Nicaragua's volcanoes would cause a lot of economic concern.