I've never had these issues. . . at least not really. I mean, unless you are running for a bunch of people whose character's you are totally unfamiliar with, how can you choose/create ACs that are so high they can't ever be hit?
I am not very good at math, and I don't think much about numbers. I usually don't know what my player's stats are. I basically rely on the game designers to handle the math.
And even if you did, let's say it was a dragon - on the fly someone could make a spot check to notice a "weak point" in the dragon's scales (for example) so that PCs purposefully aiming for that point have to hit a lower AC. . .
And then the next time my players are in combat against a balanced monster, they'll want to notice it's "weak point" and I've got something of the opposite problem.
Mostly, I wish that the 3.X designers had put something like Monte Cook's article or the table from the 4E DMG in the 3.0 or 3.5 DMG.