I said "sometimes," but it's not that often. More like, similar to what Healed said, if I knew he'd been sick or had an injury. If he just came back from a trip, I might ask, "Did you have a good trip?" (and he'll usually just something like, "yes, thanks.")
With ex-MC, when there were times he had to cancel at the last minute, I've said something like, "I hope you're OK" or "I hope everything is OK" in an email. Though I suppose that's different than just "How are you?"
It's definitely a weird relationship...I mean, a first question I tend to ask a friend (or family member) in a message or email would be "So how are you doing?"