I do it all the time - I'd find it impossible to fit as many flights into the schedule without this method - even at a 24hr airport. Works well, but I find those flights that leave at, say 23:55 and arrive at 3am take longer than others to build up to a high load factor. Given time, they perform as well as any other flight. I don't think the total amount of time your a/c spends on the ground would affect the pax. experience - after all, they'll just be flying one way so wouldn't even know - it's just a late/early flight to them.
As romeozulu says - it can make it harder to schedule a-checks but I just fly the route at the optimal times 6 nights per week and then on the 7th, come back to base at a silly hour for the a-check - so I lose some load factor on that one flight but still manage to offer a daily flight.
As I've said before - it'd be nice to be able to do the A-check while on the ground at the remote airport, like in real life - assuming it's a reasonably large airport of course.