It seems like that would be fine, but it's not. The packages will still be in the database and Package Manager will run very slowly and will crap up the error log with lots of messages about the missing files. I think it will actually download them again if it can. If you remove the files through Package Manager (Extras -> Installer), it will try to uninstall the components, sometimes messing up things in the process (depending on how well the package author has written the uninstall code).
What you *can* do, is:
1. In Package Manager, remove packages that you have uninstalled and no longer need.
2. In Package Manager, remove previous versions of installed packages (Extras -> Installer -> View Details -> Uploaded Versions -> right-click on version). That will delete the extra .zip files for older versions. Be sure not to remove the top one (the most recent version).
TBH, if things were that tight, I'd think about either upgrading your hosting package or (more likely) moving to a
MODX-friendly host.
PS: Check your error log and any logs created by extras you have. Those can get huge over time.
