In terms of the show and game, I assume they mean that he can still only enter 6 pokemon into a fight, regardless of balls. I think anime Ash carries like... 900 pokemon at any given time. He's like the implausible inventory system of any RPG.
I mean, besides like, coins, I'm not sure I could hold onto 99 of anything easily. Like, 99 potions, 99 sandwiches. Even 99 peanuts would start getting a little uncomfortable.