APCs do not fire ATGMs *properly* period. This has been a problem since CMSF came out. I have posted here and there about it since the game came out and I am surprised this has not been a priority.
If one APC is faced with another there is no reason why it wouldn't fire an ATGM, especially at a distance--if the targetting unit is not moving; yes, I understand this must be the case. If it sees a tank in overwatch, hulldown or whatever this would/should be an instantaneous response. No delay, no waiting for the AI to decide, either that or there must be an over-ride for the human player. Absolutely.
I would rather have units out of ammo than not use their ammo. Especially in this setting, where a single TOW is a guaranteed kill. Nothing like a tungsten round in CMx1.