It is common that the military (and presumably the intelligence community) have disaster scenarios, where if servers or data is potentially compromised by outside groups, that a self-destruct mechanism is activated, rendering the hard drives and memory chips of these servers useless. I’d be shocked if these precautions had not been put in place in such a sensitive operation. Typically, acid is contained within the server case, and by activating the destruction system, the acid is dispersed throughout the server, with particular emphasis on the data storage and memory chips.
Oh we invented thermite a long time ago
There are also backups.
The data on those could have been grabbed...