The PokéBall transforms Pokémon into red energy. But the Pokémon can be saved on a PC, too. And there it's saved in digital form. So I think the red energy visualized how the PokéBall scans the Pokémon.
But have you never thought about what happens to the Pokémon when it's caught? I mean the PokéBall also alter the mind of the Pokémon and make it more obedient.