Phione

I understand if I use Phione's "Whirlpool Suction" Ability and target my opponent's Pokemon with Stealthy Hood attached the effects get blocked. But what happens if later in that turn I use Tool Scrapper to remove Stealthy Hood. Would I then be able to use Phione's "Whirlpool Suction" Ability or has it already been used up at that point?

Sorry, even though Stealthy Hood blocked the Whirlpool Suction Ability it's considered to be already used. You attempt to use the Ability and the effect doesn't work, but you have still used the Ability and cannot try again.

If I use Phione's "Whirlpool Suction" Ability and target my opponent's Pokemon with Stealthy Hood attached I know the Pokemon with Stealthy Hood does not move. But would I be able to discard all cards attached to Phione and put it on the bottom of my deck?

No. Since Stealthy Hood blocks the move effect of Whirlpool Suction, the "if you do" clause fails and Phione stays in play.