Up to 2008, 100% sure. AFAIK, they were doing primarily mixed mode analogue as this stuff is harder to do inside an FPGA. I worked for one of their nefarious suppliers for a bit.

Wikipedia says they have their own fab at Ft Meade. Or is this just a super secure division of an Intel fab?

If you've ever worked in the defence industry, you will find out that you can't just ship designs to be fabbed. They are strictly information controlled and classified. That favours FPGAs as the process is externalised and the design is secure. ASICs cost at least a few million to get off the ground and you're not guaranteed your design will yield on the first run. Bringing the process in house only makes sense for very specialist hardware (think mixed mode and rad hardened) as these can't be got off the shelf.

When I worked for one of these orgs, we had a PowerPC rad hardened device which was based on a 603 and that was nearly $100k a unit in quantities of 50 and that was an off the shelf design. The one ASIC we had which was mixed mode (analogue front end and digital back end) was $25k a pop in quantities of 1000 on top of tooling and design costs of $7m.

Just doesn't add up. If its on the ground or can be bought in milspec form, it'll get used. Altera/Xilinx do this for a reasonable spend. Expect to be killed by an FPGA I programmed one day :(