With advance online check-in, I imagine it would be quite difficult for an airline to cancel a return flight if the passenger had already checked in before the missed outbound.
Not really - just because you've checked in, that is no guarantee you'll take the return flight if the outbound is missed. It's also no guarantee you'll actually get on the plane (because of overbooking).
In the case of non loco airlines, if your boarding pass isn't swiped at the gate for your outbound, a computer will cancel your booking on the return unless overridden by ground staff, whether checked in or not.