Which is the best for adjusting the size of an npc? I've always used "scale" as opposed to "height".

I suppose it doesn't matter, but the weapon changes in scale if the npc's scale is reduced.

interesting. Well, I'd suggest scale since it probably scales the NPCs proportionately.

You can't change an NPC's size with height. That's for changing the height of the collisions detection box. Use Scale for changing sizing the NPC proportionally or use ScaleZ for just changing it's height without the rest of it's proportions(basically stretching it). The weapons issue can't be helped.

read more about it here:
http://www.map-review.com/forums/viewtopic.php?t=410)

Oh, and this while this is still BETA, it might be helpful(Leslie is working on the final now, I think):
http://www.pcgamemods.com/5253)