I will give the classic "It depends" answer. There is no problem with having both types of services published to the same GIS Server Site. I have a Site doing the same, as well as a site with strictly non-hosted services. Where it depends is the architecture of your specific GIS Site and the services being published there. How many machines are in your site? How much RAM and CPU resources do your servers have? Is the Data store installed on the same server? How many/what type of services are running and what kind of demand do they have? Are you utilizing Shared instances?
You can have hosted and user-managed data-based services on the same GIS Server Site, however just like any other environment it will require capacity planning, monitoring and adjusting to make sure the services are performing at the highest level possible.
