Captain Toad's inability to jump could maybe deter Sakurai from choosing him if Sakurai actually cares about it; after all one of Sakurai's stated reasons for excluding Ridley prior to Ultimate was that Ridley not being able to fly unrestricted "wouldn't feel right". However if Sakurai wants to add Captain Toad he will do so anyway regardless of the jumping, Smash takes liberties with every character to make them functional and balanced; Ridley and Charizard can't fly in Smash, the Kirby characters don't have unlimited jumps, and Ganondorf can't float at all (and even has the worst midair jump despite his canonical ability to defy gravity), while on the opposite spectrum you have a bunch of characters being able to do midair jumps just fine that would never make sense being able to do in their own games (can you imagine the likes of Snake defying gravity and midair jumping in a Metal Gear game?).
Even as someone who is critical of the concept of Toad and Captain Toad making it into Smash, I think the whole jumping argument is nonsense and is very unlikely to matter to Sakurai.