Possibly, fairly sure it affects the sinking itself. Say in normal weather a ship sinks and lists to a point were the water is just spilling onto the decks. In heavy weather the ship will be bobbing up and down, causing more compartments to go below the waterline.
Haven't really tested in heavy weather and I tend to sit out storms (cant see through the scope most of the time, <500m visibility).
Flooding times themselfs are fixed variables though, so I don't think they're affected.
On the capsizing; yes and no. Yes, I can get them to capsize (kinda), but it completely destroys any balance in the mod. Maybe needs a different aproach.