Mount up, for ease of removing the lens from the case and getting it onto your camera, and because if the hood is a bit of a tight fit you'll have nothing to grasp to remove the lens.


Also, from a protection standpoint, the cases offer rip-stop fabric and a lot of padding. So, if you have the lens caps on both ends, it's really unlikely you'd directly damage an element either way. Instead, it will be the momentum of the lens and the inertia of the internal elements that will cause damage - i.e., misalignment of the optics is the most likely kind of damage for a lens dropped in a case like that, and for that it doesn't matter which orientation the lens is in. So, go for the convenience of mount up.