I don't think there is one answer. Try this test.

1. Backup all programs.

2. Flash and eMMC flash your N900.

3. Restore all programs.

I predict you will see a noticeable speedup, DESPITE THE FACT THAT YOU HAVE INSTALLED THE SAME NUMBER OF PROGRAMS.

This shows that the slowdown is not caused by the number of programs you have installed, but by other factors.

I have noticed that the amount of rootfs space seems to impact speed. So I close all or most of the catalogs available in App Mgr, giving me more rootfs. This seems to result in a speedup.

For other tips on rootfs, see the Wiki.