In real life, I would assume that the decreased water pressure would alleviate it somewhat. Whether the game models that, I don't know. But I wouldn't count on it stopping just because you surfaced. Even running on the surface, the majority of your boat is still in and under the water. Being on the surface doesn't stop any other kind of ship from taking water if it's damaged to that extent, and given the u-boat's low profile the decks themselves are barely above the surface most of the time and may actually be under it sometimes depending on the weather and sea state.
Many u-boats surfaced after taking damage while submerged and still sank, sometimes from the damage already sustained and sometimes because their crews caused even more damage deliberately in order to scuttle the boats so they wouldn't fall into enemy hands. So it's entirely possible for a u-boat to surface and still take enough water to be beyond saving.
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