This depends on the UPnP server running on the device. Some servers insist on transcoding all media you put there to mp4 before offering any way to play them. Others, simply offer the mkv. and of course, there the ones which can't transcode all files to mp4, so you basically can't server non-mp4 files.
One of those options is probably applicable in your case.
I was just about to post about this, I have a Kingston MobileLite Wireless connected to an External HDD. VLC on iOS doesn't recognise the .mkv files but the OPlayerHD app does.
I wondered why everything was .mp4
With more browsing, I've come across a few discussions on this, and someone has said to use nPlayer, which will allow you to use SMB/CIFT streaming which works flawlessly (You'll see every file). The only problem now is nPlayer doesn't support DTS.