I wouldn't call it a waste, but the reason to use a hab is if you don't have a commercial shipyard large enough to handle it; the primary purpose behind adding it to extremely large designs is to allow it to be constructed straight from planetary industry. I'd say asteroid and sorium miners built with orbital habs and enough mining modules to make a Vogon jealous tend to be a fairly typical design, actually, to take advantage of economies of scale. To wit, you need one orbital hab per station, but you only need one per station regardless of size. As such, if you're already making it big, make it *really* big as far as your present industrial output can handle rather than building loads of small stations with loads of orbital hab modules. If you can build it in a shipyard without an orbital hab, there's no real need to add one, though you may still want to do so if you don't actually want to dedicate such a large shipyard to that task.
I wouldn't worry too much about morale, either. It primarily affects combat and survey operations; freighters and miners don't really care unless they end up caught up in a combat operation and need to react in a hurry. It's decent fluff, though, and I'd say a lot of fun in the game can come out of RP decisions. Oh, one other thing occurred to me: while they'll work for asteroid miners, I don't believe rec facilities are as useful for sorium harvesters at present since I'm not sure if the change allowing them to function in deep space has made it to VB Aurora. In other words, a sorium harvester/rec facility, while a clever idea for a deep space tender to support farflung operations, is going to have to be able to move between the gas giant for sorium harvesting and a nearby rock where a colony can be set up to run the rec facility.