When using more than one expansion board, the modified number of players is one less for each additional board used. (In a 5-player game using KH and DH, the new modified number of players is 4.) The rules state that this handicap if for such things as monster limits and the number of gates that can open.

What about during the Final Battle? In a 5-player game using both KH and DH, does it take 5 hits or 4 hits to remove a doom token.

My guess would be that the Final Battle is unchanged. What do you guys think?

Final battle is the one thing that is unchanged. It's actually an official declaration.

The player count is reduced in order to deal with the threats from multiple boards, but when you're in Final Battle, that's no longer relevant.

Yep, it is official. During the "arkham" phase of the game it is 1 less player for all circumstances where counts matter. For the final Battle, it is actual number of players.