after the discussion with dan, he convinced me to say we do create classes even if empty: the user then is not confused where to look for them, and we are future proof. and the orm can have less feature complete classes and our other services can see if the class implements the interface or not.
if another bundle wants to extend the neutral model class, it still can do that without problems, and if the phpcr class was empty, it will lose nothing in the process.