>>2764721This is a good question. I would guess it's a combination of
1) they probably aren't submerged for very long, aiming to get back above water within a few seconds
2) they would wear a waterproof layer like you mention, but probably several other layers of other clothing underneath that. So even if the layer beneath the seal skin got wet, they could probably remove it and the layer beneath that one would likely be totally dry, due to the short duration of immersion. They also might have carried spare inner layers wrapped in waterproof material to change into, just in case.
3) they probably fished or whatever in groups, so if someone was at risk of being cold, they might have put them in a boat with someone else to share body heat. This one seems dubious to me, though, logistically, but I'll mention it anyway