Correct, I'm 98% sure that Marowak would not stop Balloon Bomb since it targets the deck instead of the hand, but it would stop things like Giratina EX stadium/tool/special energy lock, or in expanded Sesmitoad's quaking punch item lock.
Yeah, you are right. I just reread the card and it really is just the hand. Bummer. Not sure there is anything that would stop Balloon Bomb in Standard. I am sure someone, somewhere knows a card that stops it in expanded (maybe).