I'll try putting on my tin foil hat and make a guess why National Dex isn't a thing. As people have already mentioned before, the number of pokemon grew to ~1000. Moving all those to 3D would need making a good number of rigs for the models. Note that these aren't all humanoid models or have a few general body types where you can group sets of pokemons to and reuse the same rig. So you're looking at making a lot of rigs, then make animations for each of those rigs for all the moves that each of those pokemons using it can learn, plus all the non-battle animations needed when you see pokemon out of battle. I guess you can cheat on some animations by making a general casting animation for abilities that can act like spells, but still, you're making a huge number of animations for a good amount of rigs. Not only is the effort needed to create all those immense (more so if it's true that Sword/Shield was originally a 3DS thing that needed to be fast-tracked to Switch where people are more expecting with graphics), you're also looking at a lot of space used to store all that data, on top of all the textures needed for the models, and the models themselves. I have no doubt they could blow past the current limit that Switch cartridges have if they included all those, along with 3D stuff needed for the world, props, and the people in it, especially if what we're hearing is true that GameFreak aren't all that great with optimization.
For sure, they can include it in an update, but I think Nintendo doesn't want this:
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I'm not sure if they have marketing research that shows having this on the cover deters potential customers from buying a game, but I think it's very Nintendo to want to have the game playable as-is without any downloads needed.
No doubt they could add in the rest of the cast as an update down the line, but I think that GameFreak isn't even sure how big the final install size would be and how much more manhours are needed if they want to get all pokemon ever into Sword/Shield at the moment, so they don't want to commit to anything at this point. In-game, it's easier to just not have the National Dex at all instead of having one with empty spaces for the missing pokemon. Having those spaces means that players will expect those pokemon to come at some point, so it's a hard commitment on GameFreak's part.
I'm not trying to keep GameFreak blameless in all this, mind. If it is true that dynamax pokemon needed new models on top of the regular models, that's a head-scratcher. Doing the Pokemon Go approach of releasing pokemon in updates gradually might help, but that still means a hard commitment to making every pokemon appear in Sword/Shield.
Honestly, Pokemon might be better-served development-wise by being a living game at this point, but I'm not sure how well that would be received by Nintendo management, GameFreak management, and the players themselves.