If my opponent used Turtonator GX's "Shell Trap" attack and I have Magearna EX with the "Mystic Heart" Ability in play, will my Pokemon with Metal energy attached get the 8 damage counters from "Shell Trap" if I attack and do damage to Turtonator GX?

No, it will not receive the 8 damage counters. Mystic Heart prevents all effects of your opponent's attacks, and Shell Trap's damage counters are an effect of your opponent's attack.

Relevant cards

SMA_SV52