I always stayed with the upgraded early models of my boats, once I switched from type V11 to IX (late war).
I found that it is more of skill of the skipper, than the overall tech of the boat. (In my Opinion, of course

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The game is always the same when you happen on a convoy no matter what the boat.
And Onkel Karl never seems to care where you patrol, just what you deep six.
You appear worried about treacherous patrol areas. Then just humor them. Patrol at a near crawl speed, submerged for 24 hours, just to appease (if you RP it as I do, HQ don't seem to care where you go honestly)
Then go to where the pickings are good/where you feel comfortable. Empty your torpedoes, and crawl home alive.
Personal opinion ahead:
I honestly find the type IXB a little better on the e-dive than its updated cousin. Which in late war situations is important, with aircraft.
I usually roll with a top notch type VII in my late games, less ordinance, but dives faster. I tend to play more defensive than most kaleuns.