Yes, it's a foul in NCAA rules, but in NCAA it's only a 5-yard delay-of-game penalty. (7-1-5-a-3, if you're curious).
Also, according to a recent memo from Rogers, the defense clapping can be considered a foul under this rule (since a lot of offenses have gone to using a clap for as a snap count).
The umpire does monitor this, but I'd imagine that in some of the bigger/louder stadiums at the D1 level it's rather hard to hear. At the levels I work, I've yet to encounter that problem.
And I enforce it mechanically the same way for both FED and NCAA... if the disconcerting signals DON'T cause an offensive false start, it's nothing more than a stern talking-to on the first occurrence. If they disconcerting signals DO cause a false start, go straight to the Unsportsmanlike (FED) or delay-of-game (NCAA) foul.