[Sailor Steve]

They couldn't. Heavy seas were the bane of submarines in WW1 and WW2. Torpedoes could "broach", or break the surface and then dive deep and lose control, or they could break the surface and then explode on hitting the water again. Both Germans and Americans had problems early in the war with torpedoes running too deep on the best of day. Heavy seas made it worse.

According to Peter Pad field's War Beneath The Sea or The Battle of the Atlantic, by Terry Hughes and John Costello (It might be either one - it's been a long time since I read them, and neither's index is helpful in this matter), sometimes in really bad weather an entire convoy would heave to and maintain position, all pointed into the seaway, knowing that no U-boat could attack in those conditions.

As to your second question, also no. The inner torpedo loading door opens inward, and with the outer doors open the pressure at anything deeper than periscope depth could force the inner door open. On top of that, firing on a sonar bearing only was tried by the Americans early in the war and found to be much more difficult than anticipated. So difficult, in fact, that it never worked in actual practice. You would have to take a periscope sighting, and by the time you reached 100 feet or so the solution would be so old you would have pretty much no chance of hitting your target.

So submariners didn't like foul weather any more than the surface sailors did. The only difference was that the sub guys could ride out the storm in relative comfort.