Sounds like a everything points to that hip, being in foal is only going to aggrevate any hip/leg issues she has, so I would be more supprised if something didn't start to bother her as the belly gets bigger and heavier.
During pregnancy, hormones cause things to loosen up a bit, including ligmaments that aren't to do with birthing, so she could just be having more trouble on account of that. This may be an indicator that this should be the last foal she carries if it's hard on her with that hip.
Being off balance, one hock or the other is going to be overused, so I would be wary of a bone spavin down the road, esp. if her conformation lends itself to it without the hip problem.
Other than good nutrition and mild exercise, not sure there's much you're going to be able to do besides offer a good chiro adjustment now and then and some massage therapy.