Just to be sure... you know the ammo itself is free, right? You can empty them each mission, no problem.
Of course, if the ammo bins or rifle themselves are destroyed, you're not getting them back (until future updates/expansions anyway). But I found that the Highlander was beefy enough, and makes short enough work of any immediate threats, that it hasn't been in any serious danger until the post-game, when you might start facing full assault lances.