I have friends that work in scientific agencies (NIH, etc), as well as for government contractors doing science stuff.

Am I correct to be worried for the sector? The best that can be hoped for is that the sector is simply ignored. The budget for it isn't even very large compared to DoD, but it is very hard to draw a line from R&D to profit. But we've seen with other agencies the violence is the point, and I don't expect them to treat Big Science any differently.