Earlier quoted context omitted.
I'd attach them to the PCIe bus somehow, or otherwise wire them straight into the motherboard. Let me remind you that this computer can fire missiles at people , and has a potentially unlimited budget.
It does not have a potentially unlimited budget. As was mentioned above, these are often contracted third parties who develop the systems. They put in bids on government jobs and undoubtedly have their own margins to look after. Once the job is awarded, my understanding is that you can't change the price-tag it was awarded at. (At least, not easily)
The costs of good vs. bad IT security are actually not terribly significant in the context of the overall defense budget, either.
It's really a failure of process and vision, not resource constraint. Government IT and IT security used to lead industry; now consumers especially and even enterprises are more advanced than government.