Yeah I can't say I have any in my collection that are *.md
I take that back, I have one that is *.md, and I don't know if I've tried it in jEnesisDS. A good 30 of them are *.smd, and the rest (~5,270) are *.bin
Keep in mind that there is also a size limitation on what jEnesisDS will open. If memory serves, it won't open any rom over 2MB. Whether or not it will -see- the rom is a different story, that I do not remember. However, I do particularly remember that docked games like Sonic 3 & Knuckles don't work (4MB), Sonic 2 & Knuckles (3.5MB), but the standalone games (Sonic & Knuckles, Sonic 2, Sonic 3) do work.
Edit - given that my rom collection (which should be near every game ever dumped for the Genesis and Mega Drive, 5,303 files with a few duplicates and RTS information) like I said a good 30 of them are *.smd. I'd probably try renaming to *.bin, or, failing that, just redownload the roms from another website (don't ask where, that's on you). I likely torrented that rom collection a while back (again, don't ask where), and it weighs in at 6.84GB, so that might be another thing to consider.