You can't delete the program since the program lives in the system partition which is not accessible over a USB connection.
Since you stated that you created a zero length file called uninstall (case sensitive!) in .adds/nm, restarted your Kobo and NickelMenu was not removed, that suggests something is seriously hooped on your Kobo. You might want to post in the
NickelMenu: An integrated launcher for Kobo eReaders thread.
Another item is that unless you have enabled developer mode and used the factory reset from Settings => Device settings => Developer Options => Factory reset your eReader or used a
manual factory reset, the system partition will not be reset to factory and NickelMenu would not be removed.