BD used to fly exclusively from BFS but moved its operations to BHD when BHD was upgraded from being a glorified hangar to an airport. BHD courted them hard to get them to switch. During a transitional period, they served both airports but probably concluded that it was a waste of resources to do so.
I guess BHD is much more convenient than Aldergrove for the Belfast crowd, where most business/government traffic would be headed, and probably why they fly from there.