In a previous paper, we introduced functions $\zeta_r(s,a,\Delta;q)$, which are $q$-analogues of zeta functions associated with root systems $\Delta$, and their $p$-deformations $\zeta_r(s,a,\beta,\Delta;p,q)$. It is known that zeta functions of root systems satisfy certain functional relations including Witten's volume formula. In this paper, we consider $q$-extensions of these functional relations for $\Delta=\Delta(A_2), \ \Delta(A_3), \ \Delta(B_2), \ \Delta(G_2)$. We also generalize expressions of ``Weyl group symmetric'' linear combination of $\zeta_r(s,a,\beta,\Delta;p,q)$ for $\Delta=\Delta(A_1), \ \Delta(A_2), \ \Delta(A_3)$, which were obtained in the previous paper, to arbitrary root systems $\Delta$ by using an identity due to Macdonald.