It can be anodized as many times as you want it anodized. If you still want the gun to function, then I wouldn't do it anymore than twice. You maybe able to get away with doing it more than that (depending on the gun and how careful the anodizer is with stripping) but I don't recommend it.
The less amount of times, the better. Each time a gun is stripped and anodized, the tolerance or durability of the metal becomes less. This is because some of the aluminum is taken off as well while stripping the previous ano off.
The tolerances will be fine, they will change slightly, but nothing significant (we are talking like +/- 0.001"). They are paintball guns, not NASA satellites. The durability of the metal will remain the same and unchanged.