>>48908011There are two possibilities that could have been going through their heads.
1) They wanted to end an intense battle with an amusing gag to add some levity to the scene and figured that it wouldn't affect Kingdra's reputation too negativity since its constantly shown to be a stoic dignified and powerful Pokémon in all other appearances.
2) They hated Johto Pokemon as a whole and made this scene for the sole purpose of reducing one of the few competitively viable Johto Pokemon into a joke.
You can decide for yourselves what to believe.