Beedle has meant to be creepy since his introduction in Wind Waker.Beedle in Breath of the Wild (and to a lesser extent Skyward Sword)
The beetle obsession is... unsettling. He can basically teleport all over Hyrule. And he has a totally different personality on his tiny personal sky island in Skyward Sword.
He's alright in Wind Waker though.
He keeps a human skull behind the curtain in the back of his boat in that game.
Not to mention the shop with the heart piece where he proudly displays his merchandise on top of skulls.