all in one mesh is definitely the way to go.
using 1 mesh file is also heaps easier to deal with from a resourcing point of view
Especially considering that using multiple meshes (even hidden ones) gives you a massive performance overhead. It might not be so bad if you only have one mesh in your entire game, but if you are doing something like an rts with, say 100 units on screen, each with 10 animations, you are looking after 1000 objects, not even counting the trees and scenery, so it can really quickly add up.
This is not the Sig you are looking for....