I've been gaming for a long time and I don't delete my saves, ever. I'm a digital hoarder. When I finished a game, I copy the saves over to my backup drive(s) and delete them from the save location. I don't rely on auto saves, I manually save often and use quick saves between places where I manually save. I do let the quick and auto saves overwrite, but my manual saves, I keep forever.
If you're manually saving and you aren't using the auto saves or quick saves at all, try lowering the number of auto and quick saves the game keeps and see if it prunes the older ones for you. If not, I still suggest deleting them from from outside the game. It's easier and quicker, and reversible if you mess up.