Regarding the atlantic theater... Dönitz used his subs in a different way. Germans wanted to starve out england by sinking its merchant fleet and stop the imports. Their first task was hunting merchants outside in open sea. The british submarine fleet was smaller and less advanced. Their tasks were mining german ports and seting up ambushes on known rutes. They did not hunt in open sea so much.
So german submarines often found themselves ambushed when leaving or entering the ports. It was less a random meeting, the british subs were often waiting there at periscope depth dead silent. Later in the war german subs were even forced to leave and enter the ports submerged due to that threat.
In Pacific theater US subs were not an underestimated threat to jap subs. Of course because of their advantage in all areas. The crews on jap subs were properly paranoid about being stalked by US subs. They knew they had better sensors and could easily ambush them so they always went submerged through narrow streats or were submarine action was suspected.
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