Yes, there is a limit called "quantum projection noise" that determines how much frequency stability one can achieve with a single-atom clock [1]. With N independent atoms, this limit gets smaller by 1/sqrt(N), but with N entangled atoms one can achieve a 1/N scaling. This is the ultimate limit (Heisenberg limit).

[1] https://journals.aps.org/pra/abstract/10.1103/PhysRevA.47.35...