I think the scenario where you land on the map with no ammo in the gun is a bug. I’ve had that happen to me after I went through the trouble of re-arming everyone.
But I agree with Kane that that the ammo shouldn’t just regenerate.
IMO, reloading automatically from store and updating that store would be cool though. So if you come back from mission with half a clip, the game swaps your half for a full one from store.
I know it’s doable manually (minus bug mentioned above) but it seems obvious that the soldier going on mission would take the time to reload his gun on the plane at least. 