An update on this, I had my car serviced today with the a/c issue being looked at. It turns out to be a leaking condenser which will need replacing, fortunately my car is (just) still under warranty so it should be covered (subject to Honda approval), otherwise it will cost around £900 to fix.
The dealership had another Mk4 (2 years old) in the week before with the same problem, so they're beginning to think there might have been a dodgy batch of condensers with a manufacturing fault. My car has only done 9,000 miles so it shouldn't have happened. They said it was not caused by the system being under-used, so if you get similar issues make sure you get the car checked before the warranty expires.