They don’t count for overall progress.
So I explored (got all vistas etc) every map in Tyria, every map in WvWvW and I’m stuck on 98%. I’m missing 8 hearts, 10 waypoints, 9 PoIs, 3 Skill Points and 4 Vistas. For me it seems 1 map got bugged out half-way and did not count for world completion.
Yes, I’m sure I did every single map, checked it like 20 times already.