>>56968803It's always been like that both in the anime and games. I can't think of any official examples to the contrary.
The Pokedex even has it's footprints recorded in gen 3-5.
I think it's reasonable to treat it as an under-drawn design element though. It's not like Pokemon is consistent with minor detail work.
For example Jolteon's paws changed from gen 4-5. Going from no pads to one. Espeon is toeless on it's front feet except for all the times the anime draws it differently. It's really not something Gamefreak cares about.