I guarantee you there's pretty much always enough ammo (for a full team of Exos anyway). Even on Misery where everything has about a billionty HP (or shields, or whatever you want to call it).
But the harder the difficulty you're on, the more careful you have to be to ensure that you're choosing the right equipment to keep that happening. If you make too many bad choices, and then arent using it efficiently during the missions, you can indeed run out.
I dont think I've had it happen before, though I've had a couple of specific occaisions where it came close.
Out of curiosity, Zespri, what difficulty level are you playing on?