Well the NSA is probably decent at building software. 

It's not just total compensation. Working on classified stuff can be a bit of a career killer, since you can't talk about your past work when looking for a new job.

Plus there's the antipathy toward the current Trump administration, and the general moral unwillingness of many to do defense-related work in general.

Also, last I heard, cannabis use was still a disqualifier for DoD work and/or various security clearances. There are periodic ongoing polygraph tests, not sure about ongoing piss tests. The government is big; I'm sure the exact policies differ from department to department. But this turns a lot of people off.

Of course, every single thing I've said above might also be viewed as a positive by some engineers. Maybe they attract enough "true believers" to more than make up for the other factors.