This is more an extended comment than an answer.
First, in the simplest case $SL_2$, the group $SL_2\mathbb{Z}$ acts transitively on $\mathbb{P}^1(\mathbb{Q})$, viewed as the boundary of the upper half plane in the Borel-Serre compactification. The stabilizer subgroup is the intersection of the Borel subgroup of $SL_2\mathbb{Q}$ with $SL_2\mathbb{Z}$. Note, however, that this is something non-trivial, it depends on the fact that $\mathbb{Z}$ has trivial class group. There are similar statements for other number fields, where you can identify the number of cusps of the action of $SL_2\mathcal{O}_K$ on the symmetric space with the class group of $\mathcal{O}_K$. I think statements like this go back to Siegel.
Second, I can answer your question in the function field case. If $G$ is a split semisimple algebraic group over $\mathbb{F}_q(T)$, and we let $\Gamma=G(\mathbb{F}_q[T])$ act on the spherical building $\Delta_{G,\mathbb{F}_q(T)}$ associated to $G(\mathbb{F}_q(T))$, then the quotient $\Gamma\backslash\Delta_{G,\mathbb{F}_q(T)}$ is a single chamber. The stabilizer of the whole chamber is the intersection of the Borel of $G(\mathbb{F}_q(T))$ with $G(\mathbb{F}_q[T])$. Similarly, all the other faces of the chamber are stabilized by the various intersections of parabolic subgroups of $G(\mathbb{F}_q(T))$ with $G(\mathbb{F}_q[T])$. This follows from a theorem of Soulé (C. Soulé. Chevalley groups over polynomial rings. in: Homological group theory. London Math. Soc. Lecture Notes 36, Cambridge University Press (1979) 359--367). In this paper, he computes the quotient of the euclidean building associated to the valuation for the infinite place of $\mathbb{F}_q(T)$ modulo the action of $G(\mathbb{F}_q[T])$. But since the spherical building $\Delta_{G,\mathbb{F}_q(T)}$ can be identified with the boundary of the euclidean building, this also produces a computation of the quotient of the spherical building, as described above.
Taking these two observations together, I would expect (but I do not know of a reference or argument) that for $Sp_{2g}$ the quotient you are asking for is again a single chamber in the spherical building. I am not so sure about the orthogonal group case: the classification of anisotropic forms over $\mathbb{Z}$ is fairly complicated, but rather easy over $\mathbb{F}_q(T)$. This might lead to different statements in the orthogonal group case.
[Edit: I thought a bit more about this, and there is a bit more to say about the expectation voiced above. First, we can look at the analogous situation for $SL_n\mathbb{Z}$. First, the upper half-plane retracts onto Serre's tree, on which $SL_2\mathbb{Z}$ acts with fundamental domain an interval. This is another way to see that the action on the boundary, the spherical building, is transitive. In a similar vein, Soulé has computed the quotient of the symmetric space modulo $SL_3\mathbb{Z}$ (C. Soulé. The cohomology of $SL(3,\mathbb{Z})$. Topology 17 (1978), 1-22) by first retracting onto a subspace on which the group acts compactly. More recently, these methods have been used to compute the cohomology of $SL_n\mathbb{Z}$ in some range, cf. the paper of Elbaz-Vincent, Gangl and Soulé, arXiv:1001.0789. The method generally is to retract onto a subcomplex determined by perfect forms, on which the group acts with compact quotient. Looking at the concrete quotient computations in these low degrees, it is probably possible to actually compute the simplicial structure of the quotient of the spherical building.
Ok, but this is only for $SL_n\mathbb{Z}$ and certainly does not answer your question about symplectic or orthogonal groups. The case of $Sp_4\mathbb{Z}$ acting on the associated symmetric space is discussed in (Brownstein, Lee: Cohomology of the symplectic group $Sp_4\mathbb{Z}$. Part I: the odd torsion case. Transactions Amer. Math. Soc. 334 (1992), 575-596). They discuss the action, and in particular show that the symmetric space equivariantly decomposes into two components. I think this can be worked out to show that the quotient of the spherical building modulo $Sp_4\mathbb{Z}$ is a single chamber. I am however unaware of any literature dealing with higher rank symplectic groups.]
As a final comment (sorry for asking new questions instead of answering the old ones first) it would be very interesting to know if there are statements like this not just for $\mathbb{Z}$ but for more general number rings. The answer most likely depends on a lot of number-theoretic data, starting (but not ending) with the class groups of the number ring.