I enabled periscope stabilization in the settings. Unfortunately it lowers your realism percentage, but I think it's more realistic that way. The rolling and twisting of the periscope in SHIII seems too exaggerated. I never had a chance to peek through a real U-boat periscope
, but I believe they did have some kind of stabilization.
I avoid attacking convoys in low visibility, and prefer to stay on surface when attacking unescorted merchants, using the radar if available.