Is it possible to delete history entries even if GuiXT is started "hidden"?

Yes, just display the history of an inputfield with the right mouse key (or other as specified in GuiXT configuration); select the entry with the left mouse key and press "del".

For SAP GUI 7.30 and above, create the DisappearItems key under

HKEY_LOCAL_MACHINE\SOFTWARE\SAP\SAPGUI Front\SAP Frontend Server\Administration 
instead of HKCU. 

In 64-bit operating systems use
HKEY_LOCAL_MACHINE\Software\Wow6432Node\SAP\SAPGUI Front\SAP Frontend Server\Administration

For details please see SAP note 338750.