Last question first -- once the Bohrok have completed their task, they are supposed to return to dormancy. Were MN still intact and they still on the surface, they would be going back to their nests.
My guess is the krana are in suspended animation at this point, so that they can survive. So they are not awake to be contacted telepathically. And as TMOD points out, eventually the orbits will decay and they will burn up on re-entry.