They can just classify the Spore Drive and no-one living past the 23rd century except those with high enough clearance (and the long lived species) will know it exists, and I doubt every starship carriers every peace of classified material, that would be an huge intelligence risk, so Janeway wouldn't be able to find it in the database.
And lots of people know about the Genesis device, but it's never re-created.
I can understand why they would classify Genesis, given it's a fiasco at creating living planets and is however a terrible weapon that could destroy said planets.
However, those reasons don't apply to the Spore-Drive, classifying it seems as insane as cutting your own arm off for no reason. So saying they just classified it for no reason is tantamount to say that they all forgot about it for no reason. It doesn't explain anything.