Hahah, yeah it's totally a running gag. Maybe a play on how ridiculous it was in that route east of Pewter City in the oldest games where some boy just came up to you and said "I like shorts! They are comfy and easy to wear!" At least I think it was on that route. Don't know the story behind it, but perhaps it was a strange translation, perhaps the kid was really just meant to be erratic and hyped up and not really ask you for a battle as much as run into you and start battling xD
And the ultimate Magikarp teams yeah... There's one in every game, isn't there?
Funny thing is that the shortspeople show up in the manga as well, but I'm not sure we've met someone going on about shorts in the anime. Have we?