I would hesitate to call a system that lets you keep the rest of the bullets 'magic clips'. Besides which, clips are what you put in a magazine. They're used for storing individual rounds of ammunition in groups, ready to be put in a magazine. The magazine goes in the gun. A clip has no feed mechanism, a magazine does.
In real life, soldiers do often reload before they run out of bullets in one magazine. They then keep this magazine. They don't discard it. Why? To redistribute the leftover ammunition later, when they're not fighting. But with our spaceships, we have a system that does the reloading bit for us. Without knowing the exact configuration of the weapon (does it have a magazine, is it belt-fed, or what?), I don't think we really know how hard it would be for the system to load additional ammunition into the current magazine/belt/whichever. Perhaps it's the sort of system where it could just shove a few more into the bottom of it or whatever. What I do know is, there's no real reason to waste perfectly good ammunition, whether by shooting it or ejecting the magazine. At the very least, the system could always use the downtime when the hardpoints are retracted to add more rounds to the belts/magazines/whichever.
Disclaimer here: I'm not actually experienced in these matters. I just spend a lot of time on the internet and know just barely enough to sound somewhat convincing very occasionally.