This definitely falls under the "conspiracy" umbrella, but I wonder if the major fallout of how the XY anime was handled led to the deletion of Ash-Greninja.
We know for a fact that anime staff went to Game Freak to have Ash-Greninja designed, that a lot of people throughout the Pokémon media empire didn't like the outcome of the Kalos League (to the point that TPCi's president outright told the anime writers to cut their crap and forced them to change their plans), and iirc Game Freak didn't have entirely positive opinions on how the anime had been handled even before XY. I admittedly don't know the exact timeline for when TPCi stepped in to force the anime's course change, but I'm willing to bet it was after Game Freak added Ash-Greninja in a super limited distribution for Sun and Moon. GF might have realized they had no more obligations to the anime when it was decided Ash was actually being retired, so they deleted the form in Gen 8 to wash their hands of the whole thing and force the anime to follow suit in flashbacks.
Also likely because they want to have Mega Greninja down the line.
While I'm not sure all of this is true, I do think it raises some points that likely are.
Ash-Greninja's entire existence is really awkward. It seems like it was essentially made to fill in a gap left by the cancellation of Pokémon Z. They could've given Ash another mon to mega evolve to match his rivals, but then that would've overshadowed the rest of his Kalos team that he had already been raising for the entire saga. It could've been one of his reserves, Sycamore's Garchomp, or heck even Lucario, but it would've been a very obvious last-minute shoehorn as opposed to coming up with a new transformation for the Pokémon on his team already likely to become his "ace" of that region. They tied its design and name directly to Ash, making it challenging to implement into the main series (though clearly not impossible).
Idk if the Kalos league loss was forced or not, but it honestly makes sense in hindsight as a stepping stone to Ash's Alola and WCS victories. In any case, it definitely put all the hype Ash-Greninja received to a screeching halt. They gave Ash a special form just so he could match mega evolution's power and it got him to 2nd place in the league. The aura farming was absolutely still there, but it definitely still felt like "close but no cigar" for a lot of fans. Then the decision to release his Greninja instead of having it chill at Oak's so it could help Zygarde with the remaining vines was weird and very much felt like executive interference. The only other reason I can think of to do so is because when Ash found it as a Froakie, it was known for leaving other trainers. But Ash was clearly special as it stuck beside him as it evolved. It exists in the games as something akin to Spiky-Eared Pichu or the Cosplay Pikachu forms, though is way more popular because of the aura farm. It basically just existed for aura farming.
I think it's weird they memory-holed the form in Journeys-all they had to do was draw it in a flashback or two. They make reference to the bond phenomenon and tie it to his Mega Lucario. I'm not sure there was a mandate against featuring Ash-Greninja-if there was, they at least showed footage of it in the MPM opening and promo footage. Greninja and Battle Bond's inclusion in SV with no form seemed to really seal its fate, and if it's not in Z-A, that'll be the final nail in the coffin. Since the Kalos starters are likely to be getting megas in this game, I'm not sure how you'd have both those forms co-exist in a game without abilities. Not to mention the retiring of Ash's character. So yeah, I think GF and the other hands involved in Pokémon kinda just agreed to wash their hands of it and we're likely to finally be getting the Mega Greninja that we could've gotten a decade ago. A lot of this could've been avoided if they had just made it the one new gen 7 mega, or if they had just given Ash a Lucario in the XY saga like in the games. Ash-Greninja was a small part of Greninja's popularity, and it was already super popular in gen 6 before it came along. So I think they ultimately just wanted to treat it like a Spiky-Eared Pichu.