The periscope mask and other top structure would have been struck down for transit too. In reality such loads would almost certainly be sheeted over to conceal them from interested eyes. Even if there is no intel security issue regarding the equipment, it is generally desireable to conceal everything possible about the location and movement of military hardware. Trouble is that makes for much less fun as a load. No problem in principle trucking the explosive filled torpedoes around. But usually guidance, fusing and detonating components are only fitted by an armourer immediately prior to use.