There are only two Mythos cards opening gates in Y'ha-nthlei in the whole Innsmouth game, so I'd say you're really, really unlucky if you have this situation coming up in the game. Plus, one will be Evidence destroyed: all clues are removed from the board. So, whether you use FP or not, it's very likely you lose the game.
Anyway, the FP ability was subject to a very long question time and since the beginning (2009 or so) the (demi-official) answer was that FP special ability was affected by Malaise.
Tsath games are tough, but still there are ways you can reach Y'ha-etc even with FP closed (gate box, mi-go brain case, encounters, similar gates open somewhere else on the board, you can close gates thanks to encounters). So, I'd not change this
The same thing goes for Devil Reef, and I count 14 mythos card opening gates at either Devil Reef or Y'ha-nthlei, not including the cards from Miskatonic. It is true that it's a specific situation, but it is certainly not an extreme one. The fact that Evidence Destroyed! makes the game difficult if drawn at the beginning of the game in no way justifies Falcon Point being affected by Tsathoggua's Malaise. You might still win the game through strategy if you draw Evidence Destroyed!, but if Tsathoggua's Malaise affects Falcon Point, accessing Devil Reef and Y'ha-nthlei will be sheer luck.
There are, of course, other ways of accessing Falcon Point, but still all of them depend on luck, so it makes no difference. To me, in such a situation the game ceases to be Arkham Horror and instead becomes Quest for the Gate Box or a Similar Lucky Card ™, which is a game I don't bother playing. In my eyes, this rule breaks the game!