POIs used to be consolidated into 'clusters' before -- it was messy, a pain, and generally unwanted by most so it was dropped. I don't forsee us going back, especially with filtering back in.
As for removing redunant info and duplicated zone markers... report the POIs as bad on the maps.eq2interface.com website and an EQ2MAP team member will remove the duplicate. I try to clean up obvious overlapping duplicates when I see them, but POIs are user-submitted so cleanup is user-participation as well
Not sure if we can filter on the map while maintaining them in the search results... I'll let one of the guys more familiar with that code answer there, but my initial guess is 'no can do' just because of the way the filtering / search works.