Why up a Ju-88 instead of an He-111?
Higher performance, more effective defenses.
Why up a He-111 instead of a Ju-88?
Larger effective bomb load, longer range.
B-24's are the most intimidating to me (in a fighter), why does anyone up anything other than a B-24?
Fragile. B-24s are easy kills compared to B-17s and Lancasters carry more while being able to take more.
When I'm in a Ju-88 or He-11, it seems that any other bombers land more damage than I do.
What are you bombing? If you want high damage spam on landing you need to bomb town centers.
When players land bombers, are Perk points awarded considering the plane?
Or does it only go by Tonage of bombs dropped? and number of air to air kills?
Kind of. Bomb load determines the OBJ score which is what perks from objects are based on. ENY determines how many perks you get for air-to-air kills.
Do heavy bombers get points for killing GV's?
Yes, based on the respective ENY values of the tank and bomber in question.
Could a guy that flies ONLY Ju-88s or He-111s EVER EVER EVER get #1 bomber ranking?
No idea. I've never gone for ranking.