Like I said, I very much doubt many hardcore fans boycotted it. I bet 99% of them bought it but then just complained endlessly online (and the other 1% will eventually buy it). If you are a hardcore Pokemon fan are you really not going to buy the first core Pokemon game for a console? Unlikely.
Also there are plenty of people who don't buy Nintendo portables but have a Switch, so don't normally buy Pokemon games because they don't own those systems, who got this game (me for instance - this is my first pokemon game since I got Red in 1999). So yeah the expanded sales opportunities the Switch fan base affords can easily make up for any tiny percentage of hardcore fans who did actually boycott the game.
Also like I said I think we see the negative reaction in that it didn't sell even more than it has! We see Animal Crossing, a much smaller franchise, beating Pokemon's initial launch. And while in the 6 week post-launch numbers Pokemon did over 2.6 million more, again that was the holidays for Pokemon and Pokemon is known as a more launch heavy seller, and it did indeed drop off drastically after the holidays while Animal Crossing seems likely to sell far more than Pokemon during their respective second quarter of sales. That should make us realize just how much bigger Pokemon Sword/Shield could have been if it had gotten the good word of mouth that games like Botw, Odyssey, Smash, AC have all had. If Pokemon had been a critically acclaimed game it would probably be a couple million higher right now. While I think Pokemon not being critically acclaimed the way many Switch games have been is hurting it more than any hardcore-fan-only controversy, I'm sure the negative news of the controversy did play a bit into the wider so-so acclaim for the general market reaction to the game.
I couldn't agree more with this post. People acting like the vocal minority was forever shut down because they are looking at SS numbers in a vacuum aren't seeing the big picture. People did buy the game but they were disappointed and i could see this affecting the sequel moreso than SS, but also affecting the legs of SS, as consequences of these things aren't always immediate. A popular saying in the box office is that successors pay for the sins of their predecessors and i think that same quote can apply here when discussing game sales.
Every franchise is breaking its respective record on the Switch and Pokémon is looking to be a clear exception to this alongside 2D Mario which is also another IP in turmoil largely due to laziness and lack of creativity turning people off to the IP. This was also the first console Pokémon and yet the brand is no longer in the league of its own that it was during the Gameboy and GBA era or in a league with only Mario Kart like it was for the DS and 3DS Era. Its now selling on the same tier as Zelda and 3D Mario, while now likely selling less than Smash and Animal Crossing and far less than Mario Kart.
Had GameFreak delivered on the promise of this game I don't think money would have been left on the table but that is just me.