Hi bscout,
You could probably use current sensing, or if you have quadrature encoder feedback wired up, you could command a short move on each axis and see if your number of counts changes. The problem with doing any kind of closed-loop "test and verify" move like this is that if you
do have a motor connected, you might be undesirably driving it without knowing what state it's already in. But since you are making each motor find a home position before doing any other work with them, that doesn't sound like a problem.
Alternatively, you might even just have each one look for home like you are already planning to do, and if one doesn't find a home position after the standard seek process you could assume that motor/axis was not connected.