I think the problem is space. Movie cameras at that time were big, clunky affairs that had to stand on trypods. Getting it down the hatches was certainly feasible, but there might not have been room to set one up in the conning tower.
The cinematographer for
Das Boot actually created a camera specifically for that closed-in interior filming.
http://en.wikipedia.org/wiki/Das_Boot
Scroll down to "Special Camera".