There shouldn't be any issues with the setup you are talking about. The only thing that you might want to think about is the security aspect for that setup. The layers within the service will all have the same sharing access, so if you wanted to restrict one of the layers from a certain group you would be unable to do this. If each of the layers was its own service you can have finer grain control on this.
This setup should not impact the downloading of basemaps.
Russ