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My mental justification is that the Tardigrades were either extinct at that point (which is stated to have happened at some point prior to the end of DISCO S3), or what few post-Message in a Bottle admirals might know about the classified project couldn't justify making them suffer-- because, y'know, that is a thing that happens with the spore drive.
Hell, even if it was an option, would Janeway go for it? We saw her get rightly pissed at the equinox crew for running their ship off space aliens' suffering. and I feel like the next-closest alternative known at the time (genemodding someone with Tardigrade DNA and also making them suffer through the jump) might also fly in the face of her highly principled stance.
Spore drive tech is so OP that there is no possible moral argument that could ever explain its complete absence post 22nd century. Reduced usage? A secret on the same level as Omega? Sure. But totally erased from the universe? No fucking way. It's basically god-tier transportation technology and it breaks the whole universe.
Kinda want to see it still in use by Section 31 for the upcoming movie.