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I'm confused about the meaning of "modular" in the statement of the question. For example, if you have a polarized Abelian surface, then you expect that there is a Siegel modular form (not necessarily cuspidal) whose L-functions are related to the Hasse-Weil zeta function of the Abelian surface. If the geometric endomorphism ring is Z, then you expect to see a stable cuspidal Siegel modular form; whereas, if the geometric endomorphism ring is non-commutative, then you can prove that the Siegel modular form is going to be an Einsenstein series coming from the Klingen parabolic subgroup.
Thanks everyone. You can actually count the number of subrings of index $p$. Namely, if $r(x) \mod p$ has $u$ factors of degree $1$ and $w$ factors of degree $2$, and the rest of higher degrees, then the number of subrings of ${\mathbb Z}/p{\mathbb Z}[x]/(r(x))$ of index $p$ is ${u \choose 2} + w$.