[ It's so nice to see somebody else has been wearing their tinfoil hat this whole time... thanks Finn. ]

They've already been publicly undermined by Zandr's escape, and placing any significance on a missing object is only going to layer on humiliation and generate questions. Better to keep the focus on their scapegoat than draw any unnecessary attention to what that secrecy's covering up, or why the item might be valuable to the Federation.

[ It's good to know. That these actions aren't a reflection on the whole - maybe there will be people left to step in and take the reins to keep the Galaxy moving if they're successful in exposing this whole mess. ]

Kaeya implied that the Federation hadn't really known what the orb was capable of, and that the only people who officially knew about the successful creation of the new particle at the time were Brennon, Breezr and - previous to his death - Adrih. Brennon's probably tried to keep it as close to locked down as possible now they understand the orb has a wider field of utility than just synthesising particles.