The audit is for Congress. Black budgets are included and redacted. Certain members have security clearance and can see these items. The important part is that when they allocated money to an agency, it is spent as intended. The Department of Energy is audited every year, and passes. It is responsible for our nukes. The particulars are not known to the general public. The Sec. Of Energy is responsible for this and reports it to Congress every year.

They could easily redact anything that's a national secret. Musks goal wasn't to lower waste or the budget anyways, so it's kinda a moot point.