Some of that you have to remember is you're in the middle of clearing that up. From a story stand point, you've cleaned it up. HOWEVER when the game first came out, pretty sure they didn't have the tech to have your world view keep all those criminals off the street.
Later, we got some tech to do that and we see it in AP, when you complete a mission, you lose a bunch of enemies off the street.
I can't recall the contact, but if you complete all the ones in AP, I believe the last contact will talk about how you cleaned up that section of the city so well none have to worry and you are sent off to the next part of the city to work on cleaning it up.
So on and so on. People don't generally get through all those missions of course.
Some of those design choices one has to handwave away, as the meta of the game needs enemies everywhere for everyone.