Memory and Cpu does not rely on each other.. if you don't mean the swap which i do not think you do. The n900 is not a windows machine..

If the "uninstalling program" made the n900 feel faster it has to have been a bad program that caused the feeling. Maybe it had a bug or made updates of something that took cpu. As long as you don't fill up the rootfs completely it should not be a problem. A linux machine do not slow down with time like a windows machine.. thats the only logical explanation..