From what I've read, it's more to do with another mod, Unofficial New Game Plus, kind of breaking when used alongside this one? And even then, the latest UNGP version apparently fixes the issue.
But as a rule of thumb, a "simple" ship pack should usually work with a game update. Only real issue you'll get is the ships use the same spawn frequency as before, so you'll likely need to tweak that if you don't want vanilla faction fleets to spam seafood ships.
To do so, just go in the mod folder > data > world > factions and compare the rates with the ones you find in your game's core folder. It's easy enough, you'll see.