The biggest 'effect' is how they can interact. When that interaction isn't really objectionable, then it's fine.
I think I'd put that scanner antenna on top. They are usually fairly small/light, and height always helps. How much higher? Beats me, whatever you can manage. Then remember that since that scanner antenna is close to an RF source, the scanner is going to 'see' that source of RF VERY well! Hope you don't have any CB channels plugged into it, sort of...
- 'Doc