When I was thinking about a 330d I found loads of manual ones, I wouldnt say they are that rare. It is however quite rare to find a manual facelift one (6 speed / more power)

One thing to note with the diesel is the swirl flaps, if they fail and fall off they can be sucked into the engine.
It is only a couple of hundred quid to get them removed, so while not a huge issue, it can be used as a bargaining tool when buying. Not all of them are affected though, I think its the early ones that are.
Google 330d swirl flaps and you will find plenty of posts on the subject