It depends on which Unowns they have down. If you are refering to the old UF Unowns, then all of them would take Resent damage. If they have a bunch of different Unowns from DP-on, meaning different letters, then only the Unowns of the letter that KOed Shedinja will take damage. If you have a ton of one letter of Unown from DP-on then they will take damage.
Heres an example. All Unowns referred to here are Unowns from DP-on.
You have an Unown Q active and your bench consists of 2 more Unown Q an Unown D, Unown ?, and Unown !. Say the active Unown Q KOs the Shedinja, only your other Unown Q take damage, the Unown D, ?, and ! do not take damage.