[1] are there other ways to legitimately have a German flagged ship in Pearl Harbour in late 1941?
Only with some extreme PoD. German merchant ship had long been round up by the Brits, or interned. That includes German ships caught in 'neutral' US ports. During 1940 - 1941 those were somehow all sold off or seized under various legal actions. The Germans as I recall were using the money from selling the cargo ships to pay for Cash and Carry purchases in the US and S America, which they tried to smuggle back to Europe. The Brish had their diplomatic corps, MI agents, and commercial representatives in the US attempting at every turn to interfere with these German transactions. In other words the Brits and Germans were waging commercial warfare in the US and Americas.
The other obstacle to a German flagged/crewed ship in PH was the tight security. Foreign flagged ships had to ask for permission to dock there before departing another port. Whenever practical the US tried to inspect such ships before they set out for PH, and they were intercepted and inspected again by Customs and USN officers on approaching Oahu. Further, German, Italian, and Japanese merchant ships were effectively banned from US ports, with or without naval bases. The Embargo Acts severely restricted Japanese cargo ships from US controlled ports & the Germans were subject to similar sanctions.
Its not impossible for a German flagged ship to be present, just extremely unlikely.