5.3 says that when a projector fires at a hex containing multiple bugs, you make a separate accuracy roll for each bug in the hex.

5.34 says that you roll two dice after every projector shot to see if you run out of ammo.

If there are two bugs in the target hex, do you roll for "out of ammo" twice or only once?

Hello, One must only roll once, no matter how many bugs are in the target hex.  These projector shots are not very accurate, they spray things scattershot style.  So one shot hits multiple targets.  

If you watch films of projector-armed bugs on the Discovery Channel, for  instance, you can see what I mean.  Things like ants that spray formic acid, or bombardier beetles, or nasutus termites give off a spray that hits everything in the area.  An exception is the spitting spider, it makes an accurate shot that hits just exactly where it is aiming. But that is exceptional.