It's literally a requirement for TS/SCI clearance due to conflict of interest and national security. Natural born citizenship and they look at relationships fairly deeply. Even higher requirements can be needed for these positions too.
For security clearances, country of birth is not a direct factor. SEAD 4 is used as an adjudication guideline and uses a holistic approach towards clearance suitability determination. For every risk factor, SEAD 4 outlines possible mitigation factors. There are plenty of naturalized citizens (yes incl. from high-risk countries) working in IC, DoD, DoE.