Oh bless you! That did the trick, what a difference!
EDIT: Darn, I spoke to soon.
Yes it does reduce the popups when my allies are wandering around my planets (which is great), but it doesn't tackle the main problem.
1) Every time my surveyor goes to a new planet, a new popup.
2) While I'm sieging, enemy sends a new ship....new popup.
EDIT: Ok I've narrowed it down. It looks like for issue 1, the survey ship doesn't generate a popup if there are no forces there, but does if there is a civ there (even one I am not at war with). So yeah, that is a lot of my annoyance right there.