in TBOBWs it is stated that once the crew of a borg cube find themselves compromised, ie the "go to sleep trick" they self destruct.
It happens there once. Nothing is "stated", and the Borg have signed no contract obligating them to self-destruct the next time around.
Cubes may be blown up as a precaution, as in the episode "Unimatrix Zero", but they may also make a stand against a threat, or lash back in unpredictable ways. Without Seven of Nine, Starfleet would have zero knowledge on how the Borg really behave, and even Seven's testimonies have proven suspect at times.
Which is why applying an ultimate one-shot-to-kill-everybody superweapon should be done with utmost care and true rather than false confidence that it really will get the job done. Genesis won't kill all the Borg at once, as it is an effect that moves at a snail's page, allowing even wounded 23rd century Starfleet ships to outrun it. So it's probably worse than nothing as an anti-Borg defense.
Once things went boom Starfleet stepped back, looked at each other, asked "who thought THAT was a good idea" and stuffed whatever they had in a room alongside the Ark of the Covenant and Shatner's Toupee.
One wonders how many people really knew the specifics about Genesis tech. Kruge got something from Valkris, and ST4:TVH shows that the Klingons got something out of Kruge. Enough to make it futile to try Illuminati-style archiving? Or just enough to tell the Klingons and the rest of the universe that Genesis can be done, making their scientists struggle all the harder?
Timo Saloniemi