Although omnidirectional, aiming does make a difference.

"1. box at front of trunk speakers aiming forward or up through the rear deck = poor in car bass response, much better with trunk open.
2. box at front of trunk speakers aiming backward = better in car bass response by far, slightly better with trunk open.
3. box at back of trunk with speakers aiming forward = better in car bass, no difference with trunk open.
4. box at back of trunk with speakers aiming backward = best in car bass response and gets less bass with trunk open."

More:
http://www.teamrocs.com/technical/pages/aiming.htm

Also:
Upfiring causes some performance problems because the VC is no longer centered in the magnet structure. Extra wear and tear.

Must be sarcasm.

almost none, I swear.

see, since the subwoofer is an (almost) omnidirectional source, you're not really preventing a lot of excitation of the trunk lid, no matter what orientation it is in.