Separate question:
If a hero was to be protected from Underdeck abilites, would he be protected from a Topdeck ability?
Both of these abilities share a description in the REG.
They are together because the abilities have the same procedure, other than the "top" and "under" part. Since they are still distinct (they clearly do not do the same thing), they are not interchangeable for targeting purposes.
Do Underdeck and Overdeck abilities count as shuffling a character?
It is important to note that you do not shuffle the deck after an Underdeck or Topdeck ability.