XBMC has problems displaying subtitles when showing SBS 3D movies, they are only rendered once in middle of the two images, which makes them unreadable. Luckily ktrz created a patch and posted it in this thread. I build Openelec with the patch and works fairly well. By clicking the blue button on your remote or the ‘b‘ key on you keyboard it changes to 3D mode, and supports both horizontal and vertical SBS.
If you want to try the build I compiled it is available for download here.