Why on earth would they be of any use
Actually, presuming you can build them big enough, they're cheaper & faster than surface ships, since they can avoid the surface effect (waves, for instance). The question is propulsion. You really need AIP, fuel cell, or nuke (& civil nuke never caught on, since triple-expansion & marine diesel are dead cheap & almost idiotproof by comparo). And "naval crew" not an issue, either: do you think merchant sailors are hamfisted twits? It's a matter of training: given commercial subs, training in safe operation will be mandatory, or everybody aboard dies (not usually the case in surface ships...).
You then need to look at the crewing aspect. There are a finite number of men who can handle life inside a sub, even today, and subs in WW II were far worse. There is no way you could have crewed all the transport boats, much less used them to deliver the millions of troops that crossed the Atlantic during the war. You couldn't do it today with a THOUSAND Typhoon or Ohio Hulls stripped to the bulkheads, much less during WW II
If you're talking about WW2 boats, probably not. I'm not so sure something transports as big as
Ohio couldn't;
Narwhal carried 100 or so over her normal complement, & she was not quite twice as big as a typical USN fleet boat. Neither do conditions have to be ideal (& in troopers, they weren't); presuming transport subs are (about) as big & fast, & as immune to U-boats, as
QM, how many would it take? Just as a rough guess, taking a 20" bunk, 18" overhead/bunk, & swapping
Ohio's missile section for bunk space, & 3 decks, I make that roughly 20-25000.