No, they are not "clean". Moreover when you do uninstall, no files are deleted, Eclipse would just prevent plugin from loading on the startup. If you really want to remove the plugin you need to
- Uninstall it via UI
- Delete the plugin files in the file system
- Remove plugin settings from workspace or create a new one.
Here is some interesting info for you:
There is no mechanism within Eclipse to permanently and physically uninstall a feature and its plug-ins. The process to physically and permanently remove an undesirable feature and its plug-ins is a manual process that should be done when Eclipse is not running. In order to do, you will have to manually remove the files there associated with the feature from the eclipse/features directory and its plug-ins from the eclipse/plugins directory. Be very cautious as to which files you delete, and always have a backup of your Eclipse directory. If you remove the wrong files from these directories, you may have quite some trouble restoring your Eclipse to a stable state. Therefore, unless your hard disk storage capacity is extraordinarily limited, it is recommended that you simply leave the physical files in place.
Note that when manually removing plugins as described above, it is likely that some metadata will still cached by Eclipse. This can lead to problems later on. Running Eclipse with the -clean option may help with that, as it causes Eclipse to clean the cached metadata. See the Running Eclipse help page for details about this option.
Source: http://wiki.eclipse.org/FAQ_How_do_I_remove_a_plug-in%3F