We provide further details on atom number fluctuation during spin-mixing dynamics inside an $F=1$ spinor condensate, based on the effective quantization approach we reported earlier [L. Chang et al., Phys. Rev. Lett. 99, 080402 (2007)] for the semiclassical nonrigid pendulum model in terms of the relative phase and the atomic population in the magnetic $(B\text{\ensuremath{-}})$field insensitive hyperfine state $|{F}_{z}=0⟩$. Many features of the classical nonrigid pendulum model are reproduced. In addition, features typically associated with full quantum simulations specific to our model system, such as atom number fluctuations both in stationary states and during the dynamics of spin mixing, are faithfully revealed with our effective quantization approach. We check the validity of the effective quantization theory by performing extensive numerical comparisons with the results from full quantum many-body simulations. We study the effect of quantum coherence in our system and provide a solid theoretical basis to resolve the resolution limit in counting atoms that is needed to clearly detect quantum correlation effects in spin mixing.