It's generally a bad idea because the package names will still be stored in the DB and you'll get a lot of errors in the log and possibly delays in loading Package Manager when MODX looks for the files.
If you want to regain the space, the safest thing would be to progressively uninstall and remove all versions of the package, then re-download and re-install the current version.
You could delete the package and the corresponding record in the modx_transport_packages table, but I'm not sure what the side-effects might be.
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PLEASE, PLEASE specify the version of MODX you are using.
MODX info for everyone:
http://bobsguides.com/modx.html