How do the GMs out there handle it?

Determined by the ammo's availability rating, population size, anything else?

Is the target # influenced by the amount wanted, # of successes go from individual rounds, to clips, to crates?

Probably better off asking this over in the Rogue Trader forum, since Profit Factor is solely a Rogue Trader mechanic.

Acquiring a weapon, or a large number of weapons, includes ammo enough to supply it/them without problems. If you're trying to requisition weapons plus an ammo which is rarer than the weapons themselves (Man Stopper Rounds or something, being used in mediocre weapons), then your GM may either make you use two acquisition rolls or they will simply use the higher of the two and then take a -5 to it (see page 271 of the Rogue Trader Core Rulebook for all sorts of rules on acquisitions).

The only time you have to make rolls to see if you have enough ammo and such are special circumstances, covered in the section on Upkeep. It is generally considered that you can replenish your ammo whenever you return to your ship. Whilst in the field, you can either follow the "rule of three" reloads kept on your person, or modify your load-out more specifically.

Hope this helps.

<EDIT Double Posted, not sure how that happened, sorry.>