The original problem solves in the positive: there is a model of ZFC in which there exists a countable OD (well, even lightface $\Pi^1_2$, which is the best possible) set of reals $X$ containing no OD elements. The model (by the way, as conjectured by Ali Enayat at http://cs.nyu.edu/pipermail/fom/2010-July/014944.html) is a $\mathbf P^{<\omega}$-generic extension of $L$, where $\mathbf P$ is Jensen's minimal $\Pi^1_2$ real singleton forcing and $\mathbf P^{<\omega}$ is the finite-support product of $\omega$ copies of $\mathbf P$. 

Jindra Zapletal informed me that he got a model where a $E_0$-equivalence class $X=[x]_{E_0}$ of a certain Silver generic real is OD and contains no OD elements, but in that model $X$ does not seem to be analytically definable, let alone $\Pi^1_2$. The model involves a combination of several forcing notions and some modern ideas in descriptive set theory recently presented in *Canonical Ramsey Theory on Polish Spaces*. Thus whether a $E_0$ class of a non-OD real can be $\Pi^1_2$ is probably still open.