Personally I don't mind sleeping in a bunk bed, although I don't like the top bunk if there's a ceiling fan in the room :)
I know of quite a few hostels that make a big deal about not having bunks but I really don't think it is an issue as long as the place is clean and secure and there's a good atmosphere in the common areas.
If I ran a hostel I would certainly have bunk beds.
Make sure the bunks are sturdy - narrow metal frame bunks squeak a lot. Solid timber is good to sleep in but bed bugs live in wooden beds. Your best bet is heavy duty metal bunks.