If Nomad is already messed up without this change, then it doesn't matter much whether it's reverted upon hitting Castle Age or not. Regardless of what you think of WK water, the fact of the matter is that the Feudal Ships are here to stay. That is the premise you have to work with when thinking about balance changes.
Also, units getting buffed upon reaching an Age is a very intransparent mechanic that shouldn't be overused. It's done in case of the scout units because you get them from the start and they shouldn't be too strong in Dark Age. For ships there is no such reason.
If anything, it should be the Fire/Demo Ship upgrade tied to Castle Age instead of War Galley. Whether that's a good idea though, I have no clue.
Also, units getting buffed upon reaching an Age is a very intransparent mechanic that shouldn't be overused. It's done in case of the scout units because you get them from the start and they shouldn't be too strong in Dark Age. For ships there is no such reason.
If anything, it should be the Fire/Demo Ship upgrade tied to Castle Age instead of War Galley. Whether that's a good idea though, I have no clue.