My knowlegde of usb is limited, but currently the n900 draws about 18ma in device mode propably through pullup detection resitors (1.5K+15K) when conneted.
But it may even drain the battery fast if you just connect it to an unpowered host.

I heared usb 3 tried to improve on that. usb was never really low power.

On top of that the n900 usb hardware stack is "unique" and not simple (there may be bugs).
The n900 usb plug is in a bad spot and not robust.

Some kind of relays maybe a solution to disconnect and connect the devices. Maybe ask someone more involved how it should be done (joerg_rw for example).

There are still very few powerefficient affordable fast small linux boards. Most arent good at idle powerconsumumption and you cant turn them off cause linux still needs so much time to boot.

There is the rumor that someone used a setup with a n900 and some type of other external compute modul for some time, but i could not find any further information on that.