Interesting:
It seems, that for displaying new custom (copied) transaction types (Z... or Y...) it is necessary to add them to DNO_CUST04, and maintain the correct channel CRM webclient UI (http://service.sap.com/sap/support/notes/2222339). This makes sense.
But to hide a transaction type from the creation popup, it is necessary to set it "Inactive" (http://service.sap.com/sap/support/notes/1918666). It is not sufficient, to remove the entries from DNO_CUST04. This doesn't make sense, from my point of view.