There has long been a bug in the Hide and Seek form of the investigation process and since it's recently been fixed, the cockroaches are now coming out of the woodwork. It's not all your fault I'd say.
A popup would be rather intrusive if you're at war and racing to see a particular spot, which may not be something you'd experience much when not playing simultaneous turns but on a game with ST, beginning of turn pops can REALLY frustrate. That would also introduce a huge effort - not an easy thing to establish.
However, a screen like that would be nice... like an adapted military advisor perhaps.
What I've been doing lately that works for me is just reviewing the message log. When I see the message that a criminal has been investigated, which stands out nicely with the color it has, I just doubleclick on the message itself in the log panel and it takes me directly to the city it's talking about. Has been working quite effectively for me to stay on top of them.