In the "Innsmouth Horror" rules it says that:

"The rules are unchanged when using more than one expansion city, except that the number of players should be counted as being one less for each expansion board in play beyond the first. So, if six players are playing a game using both Dunwich and Innsmouth (for a total of two expansion cities), they are counted as having one less player, for a total of five players. This modified number of players is used for such things as the monster limit and the maximum number of gates that can be open at once, and it reduces the level of difficulty for the players since they have so much more ground to cover."

Does this reduction in the number of players also count against the number of successes required for each doom token on the Ancient One sheet in the final battle?

No, The imposed handicap is a result of the investigators having to cover more ground. In final battle, they're not covering ground. It would make the final combat too easy.

Tibs said:

If it did count, it make final combat with two investigators and three boards problematic.

Even so, the rules say "to a minimum of 1 investigator." So now imagine what it would be like with 3 investigators and all boards, if the doom tokens were easier to remove.

Tibs said:

Thanks! Then we've been doing it right. The rules are a bit vague when stating that the "modified number of players is used for such things as…", so a friend made me ask here just to be certain. =)