I assume the author knows why they're called U-boats, but the fact is that modern English speakers don't call them U-boats unless they mean very specifically German World War II submarines and maybe not then.

I would use "U-Boat" but only in the same way I'd use "Boomer", to indicate a specific type of vessel in a particular context, if I meant a submarine, such as in a simple drawing, I'd say "submarine" and so would other English speakers I know.