I've been researching this topic and I can't find anything but proof after proof that the Cap'n could very well be Captain Hook.

Not much proof.
Its a IP thing, and doubt they will use him. But he maybe imspired to be close, since the only proof is he appears to be a smoker, could have a hook (or skeleton claw) and is just known as "Cap'n"

I don't think they'd tie one of the main villains of their own IP to something Disney owns.

The POTC and Monkey Island stuff is set up to be able to be cut from the game completely without much of an issue if the license expires and/or is not renewed.

The Cap'n was written in well before the deal with Disney so I doubt they are written in as Captain Hook. It could be that he has some aspects to Hook but lets face it, Most pirates can sound like Hook ;)

I do however hope for Captain Hook to make an appearance one day with further Tall Tales crossing over!