Do not know about the British boats, but the US boats had two sanitary tanks that the heads dumped into. These tanks were within the pressure hull, so they were usable at any depth. There were "blown" overboard daily, when the boat was surfaced. The US boats also had what was called an 'air expulsion head' in the after end (either motor room or torpedo room) which was only used above ~100 feet; the small tank required that it be expelled after each use.

In short, the US boats never had a problem with head use while submerged. In other words, they just had two very large buckets within the pressure hull.