Well actually Z coordinates will have to be mapped manually. As we talked on ICQ ... a 3d grid is the same as if using a mesh with each node being a point in the mesh.
Overland maps for a normal zone in DAOC are generated via 256 x 256 points.
Normally you can assume that a mob can walk any path on a overland map.
The only thing you need to take care about are as you said, areas where mobs can not enter (keeps are a good example).
To use pathing inside dungeons and keeps it is different. You need to map the valid positions, not the invalid ones and connect them. Almost like a floor-plan.
Now inside a dungeon it would work like this. A mob wants to go from A to B. It searches a path-node near B (the closest one), then it searches the closest path-node near A and then it calculates the path from node A to node B. So far so good, no problem here in dungeons if they are mapped nicely
Back to overland and keeps. To map a keep you would need to define a circle of nodes around the outside (perimeter) and a circle of nodes on the inside of the keep. The outer perimeter and the inside nodes are connected through the keep-door.
A mob wants to walk from somewhere out of the keep to inside the keep, perhaps even up a tower to the lord. It works like the dungeon (almost). It searches a path-node near the lord (node A) and then it searches the nearest path-node to himself (node B). Imagine the mob is at the backside of the keep (miles away or close does not matter). It will find a node near the lord, it will also find a node at the backside of the keep (remember the node-circle around the outer wall?). Then it will calculate the path between those nodes. This way it will go around the keep, through the door, up the stairs, etc...
The only trouble is that those nodes in dungeons and keeps need to be manually placed. Perhaps it can be done with a script that places nodes on the ground in regular intervals when you run. When you come close to a previously placed node the script could automatically connect them (if they are not already connected). This way you could build up a grid by simply running through the dungeon, visiting possible places and routes.