I'm not the expert, but ... I believe trying to get subtitles from the video has little to do with Subsonic itself, but is a function of the transcoding parameters that would need to be defined for ffmpeg to do that. In that most users will not be using subtitles, the default transcoding does not perform that function.
http://www.ffmpeg.org/ffmpeg-doc.html#SEC10 Fortunately, Subsonic allows any user to customize the transcoding definitions to their own particular needs. Unfortunately, not all of us are competent enough in this area to do it properly. All the information to do this sort of thing is available on the web, and there are a few users who visit the forums who do have the expertise to answer your questions regarding the transcoding specs.
In any event, I'm guessing that you are trying to transcode movie videos if you're talking about subtitles. If you read through these forums regarding video playback through SS you should find several posts that give you a realistic view of the video playback capabilities of Subsonic. Those capabilities are not a function of SS per se, but are more correctly a function of the hardware and software configuration and capabilities of the network hosting SS. Some users come to these forums and complain that they can't get a Blue Ray that they've just ripped to play on their Android device. Duh ... no kidding, it just isn't likely to happen, especially when you're hosting SS on a single core Atom nas device with a dial up connection.
On the other hand, if you preformat your video into mp4 or flv so that it will play directly in JW Player without transcoding and you pump it out over a gigabit lan to FIOS 35 Mbps upload connection, you can achieve some pretty impressive results. I routinely stream blue ray quality hd video internally using SS and can even do so externally with a good laptop if I have decent download speed at the other end. Getting the results that your configuration is capable of takes a bit of research and experimenting, but the limitations you encounter are not a function of SS, but a function of how much end to end horsepower your unique configuration has.