The tube is low on ladies' bikes for the skirt.
Otherwise, structurally, it is better to have the top tube higher. You can make the bike lighter with the same strength.
One should not be in a large danger of hitting the top tube with testicles or pelvis (which seems more likely to me and is very painful for either sex) if one selects the proper frame size with the correct standover height. Of course, if you are unlucky, it can happen, but there are many other ways how to crash and injure yourself that are more common.