Why does the Federation classify the Omega particle? I mean, it's incredibly dangerous, but if it works? The possibilities are endless.
Because the Federation is vary of technologies whose advantages are outweighed by how dangerous they are. They were already willing to mothball the spore drive at the start of season 2, remember, and only relented to it being used again to investigate the signals. The use of the spore drive (which was actually already classified at the beginning of season 1, when it was still Stamets and Straal's pipe dream) has several inbuilt disadvantages:
1) You need a living navigator. You get one of those by torturing tardigrades (of which the Federation after frantic searching never found another one of), or by genetically modifying a human (which is against the law, even if you had another tardigrade sample to use).
2) Reckless tapping into the mycelial plane can endanger life itself. We saw that with the rot that mirror!Stamets caused with his experiments. That's a pretty big risk, especially given that
3) The two experts regarding the technology, Straal and Stamets, are dead (allegedly in one case). They were very specialized in their fields of study and research, so unless someone unclassifies their research notes, people might not even know where to start.
4) As far as Starfleet knows both ships with this technology were lost with all hands by it's use (again, allegedly in one case). That's 0-2 as far as Starfleet knows, not to mention all the other spore drive related stuff, like the aforementioned danger to all life, vanishing into parallel dimensions for nine months while a war rages, or creatures from the mycelial plane abducting starfleet personnel, not to mention the two(!) separate occasions in which the Klingons almost got their hands on a spore drive outfitted ship.
Why put more time and resources into something so fickle, when you can put the same effort into improving more reliable tech you already have?