but having the threat go up 1 for each monster that can't spawn is good enough for me and makes things nice and difficult
IMHO This tends to get way more dangerous than increasing the number of minions.
I once ran into the problem of running a two-lair-tile and having run out of minions witch resulted in an endless darkness cycle. Just adding more of them isn't even a threat as there is a maximum number of spaces from which they can hit you. The rest just stands around looking stupid.