Thanks for all your replies. I was afraid the only way to go is to modify the templates - something I will probably choose not to do just to get the namespaces I want.
The reason I want both value types and entities them in the same namespace is really a matter of personal preferences more than anything else. I never used distinct namespaces when hand coding and was wondering if I could keep it this way. I don't really like EntityClasses or ValueTypes - too much details IMO - I prefer to have it all in a *.Model namespace (one less using ).
All in all not a big drawback and I'm still happy with NHibernate support so far, so I guess I'll just have to get used to it.