^^^^ Yeah, it's sometimes three.
As for getting their plays off, that's generally unrelated to the noise (although I'm sure the noise doesn't help). We know this because they're good for burning a couple timeouts/getting DOG penalties a couple times a game, and that happens both at home (where noise is never a factor) and on the road (where it sometimes is).
Basically there are four things going on, IMO:
1) Compared to other teams the 9ers have an extra step in getting the play in: Roman calls three plays and relays those three plays to Harbaugh, who then relays two plays (and occasionally three) to Kaepernick. Most teams either have a HC who is just calling the plays, or an OC who is relaying plays directly.
2) As they're putting in multiple plays, that just takes longer too.
So, before they even get to the line, there's rarely more than 10-15 seconds on the play clock.
After that, Kaepernick is reading the defense and picking a play, which takes some time, and:
3) The 9ers basically abandoned the massive pre-snap shifts that was their signature up until right before the first game against the Hawks this year. They were phasing it out, but it's gone at this point. Still though, on most plays they shift, not only to change to a new play, but also to parse out if the defense is in zone or man. This also takes time. Some timeouts also get burned because invariably some folks mess up their shifting sometimes.
4) Teams have realized what is going on and have gotten much more aggressive about showing false looks at the line to force the 9ers into inopportune plays (as they should, and as is predictable). The Panthers did a great job of this, actually. Basically, you "show" really late (e.g. a blitz), and then force the 9ers to call a timeout, or to try to quickly change the play again, and then at the snap you drop the "blitzer" back into coverage and nuke what they were trying to do. I'd be surprised if the Hawks, who are well coached, don't do a fair amount of this.
I think these are the reasons why the 9ers are usually snapping the ball right as the play clock expires, and are a second or two late a couple times a game too. Noise obviously doesn't make it any easier, but it's an entirely consistent problem, not a noise dependent one.