Ships that have the MM designation were skinned (or painted) by Rafe Bligh - his "weathered ships" mod - and put into the game as individual ships by MuddyMonkey, hence the "MM". There are quite a few of Rafe's ship skins, and they are really nice!
"BR" means Barbarossa, the name of the famous Arabian pirate who sailed in Xebecs in the Mediterranean. The Xebec BR I believe was painted by Suraknar. There's only one "BR", nicely and appropriately historic with its Arabian paint scheme.
"CT" means ships painted by ME, CatalinaThePirate. <img src="http://www.piratesahoy.com/forum/style_emoticons/<#EMO_DIR#>/icon_mrgreen1.gif" style="vertical-align:middle" emoid="
" border="0" alt="icon_mrgreen1.gif" /> There are only two, the Lugger CT and the Xebec CT (which is the `Irish-themed` Xebec). I know, why paint up the lowly lugger? Well, I grew immensely fond of that little ship when I first started playing the game, and so that was the first one I decided to try to paint when I first started playing around with modding PotC back in February of this year.
I've done a couple of MOW skins, but have yet to put them into the game... <img src="http://www.piratesahoy.com/forum/style_emoticons/<#EMO_DIR#>/dunno.gif" style="vertical-align:middle" emoid="
" border="0" alt="dunno.gif" /> BUSY! <img src="http://www.piratesahoy.com/forum/style_emoticons/<#EMO_DIR#>/icon_mrgreen1.gif" style="vertical-align:middle" emoid="
" border="0" alt="icon_mrgreen1.gif" />
AFAIK, there are no differences in ship stats (except the typical), except I think the XBR and the XCT have pretty good capacity and speed. Otherwise, the designations are just for different ship skins.