Depends on the aircraft, and/or the route. I can only speak as a S/H driver but with sectors of only an hour or so, you can normally hang on until the other end, where you can have a slash during the turnaround or back at the crew room.
On long haul flights, there's usually not that much going on in the cruise so you disappearing off once an hour isn't going to be a problem, apart from maybe odd looks from the pax if the only loo is at the back.
But bear in mind the gymnastics required in something like a 737 to get into the damn seat in the first place you might want to consider skipping coffee. Once you've had the speedbrake lever and the odd thrust lever up your a** a few times you'll soon learn to drink too much!