Short answer: It depends on the client that you're streaming to, but generally no, any h.264 video stream is not transcoded unless your network isn't capable of streaming the bitrate of the source file.i may be wrong, but doesn't Plex transcode files? ie translate mkv source into mpeg2 streams for older devices. If so, that is pretty terrible and you are losing video/audio quality. Something you should definitely see, maybe play plex shares with videolan or something that lets you see the exact stream quality and settings, and compare that to the source MKV file.
Long answer: The Plex transoder can demux MKV files on the fly and transcode only the parts that need to be. Typically this is the audio portion, unless your client device supports both AC3 and DTS. For instance - I typically stream to a Logitech Revue which supports AC3 (Dolby Digital), but not DTS. So any of my MKVs with DTS are transcoded in real-time to AC3, but the h.264 video is left untouched. The caveat to that is that Android-based clients don't support subtitles so if you have them as a separate file in the MKV (most Usenet/Torrented MKVs are this way) and select the subtitles, the video has to be transcoded but I'm not certain what format it gets transcoded to.
FWIW, I didn't notice any quality difference when I selected subtitles for Star Wars I/II/IV/VI and streamed them vs leaving the alien dialogue off so that Plex played it without transcoding the video. These are from the blu-ray box set that I personally ripped from my collection without any compression (~35GB MKVs). I can dig through the Plex server log to see what it's being transcoded to, but since the quality didn't noticeably change it didn't bother me.
Aychamo - Regarding your question about shares, Synology is everything that a 'dumb' NAS is (zfs, unRAID, etc) plus a front-end web GUI so it's capable of any type of share those systems are plus the extra fluff. I guess QNAP would be it's direct competitor, but from my understanding the GUI is nicer on Synology and there's more installation packages available for different programs like Plex and SABnzbd.