Does anyone know if its ok to connect a navmesh down cliff drops (not necessarily just cliffs, any place where the player can drop down), so NPC's will drop down, but won't try and go back the same way and get stuck.

No you don't connect it, but mark two edges as a drop

See here:
http://www.creationkit.com/Category:Navmesh#Navmesh_Data

Its quite similar to Left For Dead's Navmesh pathing system in some ways. which had one-way connections for drops.

Good to know, thanks.