Sounds like you need to be more selective about what mods you keep. Decide on a minimum threshold of some kind and sell everything that doesn't meet it every time you get new mods. After I started doing that, I never hit the limit again. Right now I'm at 285/500, primarily because there's quite a few mods in my inventory that I should sell, that I just haven't yet for various reasons. If you're actively working on your mods at least once a week and you have a strict enough set of requirements for what you'll keep, you'll never hit the cap.