Right, scientific and technical people will get extra scrutiny. Under the US's threat model -- moral or not -- it is not the janitors and artists you worry about, it's the people visiting our nuclear, biological, and high-technology facilities.

The fact that this has very bad side effects on technological progress is important, but it's not like the government gives smart people scrutiny because it hates smart people. This behavior is brutally rational if you just look at their primary mission.