The feds can intercept the patent or even the prepatent steps before it becomes public and throw it behind a classified, very black curtain. The patent owner, if the feds choose so, will not even know what the feds are or are not using the patent for. As the patent owner, they will be paid royalties.
A company I worked for had a unique product for its time, that had a ridiculously fast microprocessor. Basically, we were about 20 years ahead of IBM and AMD hadn't even been born yet. It was equally expensive.
The corporate strategies were 1) to not patent and instead go proprietary and 2) to never sell our products to a federal agency of any country.
Our microprocessor and ROM were encased in an epoxy block plus I think had some self destruct electrical provisions as well. Basically, the idea was if anyone tried extract the microprocessor/ROM or tamper with them they would just have a useless piece of semiconductor that could not be reverse engineered or decoded. It worked.
I've filed a number of patent disclosures over the years. No patent applications were filed however. In some cases, the corporate patent lawyers declined to pursue a filing and in others the corporation decided that its best interests were served by keeping the info confidential.
In that case, why would the Navy even bother to file for a patent? Talk about national security concerns!!!