Yes, they no longer disappear. The big change for v2.0 is that NPCs are now persistent entities across maps. They can travel to any map so it would be unusual for them to disappear from the map entirely. The way I handle bed-time routine is to gate the transfer event to their bedroom to prevent the player from entering at night.
NPC coordinate reference is not really within the scope of the plugin but you should be able to do that easily with a controller parallel event. You can use this script in a conditional branch:
$gameMap.event(EVENT_ID)?.x === X && $gameMap.event(EVENT_ID)?.y === Y
EVENT_ID → the event’s ID on the map
X → event's X coordinate
Y → event's Y coordinate
Hope that helps!

