Why are Sponges and Powder Puffs, of all items, used for defense? Because they absorb the attack!
On the other hand, why would a powder puff be used to absorb things? It's used for putting on makeup (it technically does "absorb" the powder you would then put on your face, but still).
Why are disco-dancing Boos in the Enigmansion? Because disco is dead.
Kersti's name can be rearranged into Sti(c)ker. This makes sense as she sacrifices herself so Mario can use her as a sticker to win against Bowser.
In the harbor, a Toad mentioned how a ship and its crew of Toads hasn't been back for a while now. On the last level of World 3, you see the remains of the ship. With nobody remaining. The only other person you see on the island is Gooper Blooper. Think about it...