Since the thread is already using up sizeable quantities of handwavium, what's a little bit more, right?
There were proposals to launch V-1's from U-Boats as soon as the things were developed. Supposedly, inter-service rivalry between the Kriegsmarine and Luftwaffe made it a non-starter. Suppose, though, earlier 1940 use (and "success") convinces enough in the high command that a shotgun wedding is in order. Historically, the amount of time it took to develop a submarine launched Loon missile was about two years - in a post-war, low-priority environment. Put the right fire under that kettle, and maybe there are U-Boats with V-1's by early 1941.
This is still in the "Happy Time" for the Kriegsmarine, when nighttime surface operation wasn't a death sentence.
Now, the V-1 would be useless against shipping, period. Even with some clever pressurized containers for decktop storage, I can't see having a payload of more than four V-1's on a U-boat - and reloads would have been agonizingly slow. But, have a wolf pack of 10 or 20 boats launching a barrage from the North Sea towards Birmingham, Manchester, etc at dusk, only to then slink away towards Norway or Denmark to reload.
Maybe utilize the V-Boats to bombard St. Johns, Newfoundland to attempt to disrupt convoying
Once the US enters the war, the tactic could be used briefly against the Eastern Seaboard. I say briefly, because the first few barrages would stir up a huge hornet's nest. The V-Boat menace evaporates pretty quick for the same reasons it did IOTL - the advent of long-range patrols, radar, sonar, etc. But if the goals are to disrupt normal operations, divert energy and resources from other priorities, and panic populations...