Rift is all about map control and when a team is attacking they have control of the majority of the map. On most maps the heavy ammo spawns halfway between spawns so the team attacking gets both heavy crates easily. Therefore putting the defending team at a massive disadvantage. This isn't a problem on maps that have a heavy crate near to each teams spawn.
I think moving the heavy crates to the spawn points would be better than removing it.
They are fine where they are.