My guys are all indoors and haven't been exposed to new cats in more than two years--and sniffles still occasionally make the rounds. I had a litter of kittens born indoors and never exposed to outside cats that developed a nasty gastrointestinal bug--the vet couldn't figure out how they got it, just a random virus. They gave me a scare but they all got over it.

The point is that kitties will get sick, and in multicat households illnesses will go around. Balance the occasional URI against the good you're doing in saving cats who might otherwise not have a chance.