Good question! I never thought about it but in the planning I always envision a single boat. Should we limit that mission to one? After all, there were no wolfpacks in Scapa Flow....
How would you have 2, 3 U-boats in the mission? From a historical stand, one should be all.
Now, I can totally see having a harbor penetration mission where 2, 3, 4 subs start off at different points and have to detect the openings past the harbor defenses (block ships, asw nets, minefields, coast patrols, nearly invisible fishermen with flare guns...) and use their enigma to decode incoming intel (clues) in a race to get in first and sink the target.