A structural study is presented on proton exchanged LiNbO$_3$ waveguides prepared in benzoic acid vapor which, for $z$-cut substrates, were previously reported to simultaneously exhibit high index jump, very low losses, and undegraded nonlinear optical coefficients. X-ray rocking curves of $z$-cut guides show a unique, intense peak with the same bandwidth as the substrate peak, located at the $\kappa_2$-phase position of H$x$Li${1-x}$NbO$_3$, as well as a small $\alpha$-phase contribution. For $x$-cut guides only the $\beta_1$-phase peak is obtained, with a bandwidth about 60% greater than the substrate peak. Distinctive features of $\kappa_2$ and $\beta_1$ guides are also shown in micro-Raman spectra.