> The NSA isn't an independent agency, it's a part of the US military chain of command under the Department of Defense and hence is under the direct control of the Command in Chief.
The NSA's existence, as well as some particular details of officers that it must have, etc., are mandated by Congress in statute; see the National Security Agency Act of 1959 (and subsequent amendments thereto.) That it is within the military chain of command doesn't change this; Congress's power to do direct the structure of the military is an enumerated power in Article, Section 8. The designation of the President as Commander-in-Chief does not make the President unreviewed dictator of the military, it simply restricts Congress power over military organization such that the Congress cannot place authority to command the military within the regulations adopted by Congress in some other person than the President.
Congress's power to direct the existence, function, organization, and funding of agencies -- and the President's lack of Constitutional power to disregard Congress's directions on those matters and disband statutorily-mandated programs and agencies -- is not, contrary to your description, restricted to independent agencies. It absolutely does extend to federal executive departments, including the Department of Defense.
> The head of the NSA is always an active enlisted officer who is part of the of the joint chiefs
No:
(1) The Director of the NSA is always an active commissioned officer (and a four-star flag officer during the tenure in the position.) Commissioned officers are not enlisted personnel.
(2) The Director of the NSA is not a member of the Joint Chiefs -- the Joint Chiefs of Staff include the Chairman and Vice Chairman of the Joint Chiefs, and the Chiefs of Staff of each service (Chief of Staff of the Army, Chief of Staff of the Air Force, Chief of Naval Operations, Commandant of the Marine Corps, and the Chief of the National Guard Bureau.) The Director of the NSA is Chief of the Cyber Security Service, but not every position with the word "Chief" in it in the military is a member of the Joint Chiefs of Staff.
The NSA's existence, as well as some particular details of officers that it must have, etc., are mandated by Congress in statute; see the National Security Agency Act of 1959 (and subsequent amendments thereto.) That it is within the military chain of command doesn't change this; Congress's power to do direct the structure of the military is an enumerated power in Article, Section 8. The designation of the President as Commander-in-Chief does not make the President unreviewed dictator of the military, it simply restricts Congress power over military organization such that the Congress cannot place authority to command the military within the regulations adopted by Congress in some other person than the President.
Congress's power to direct the existence, function, organization, and funding of agencies -- and the President's lack of Constitutional power to disregard Congress's directions on those matters and disband statutorily-mandated programs and agencies -- is not, contrary to your description, restricted to independent agencies. It absolutely does extend to federal executive departments, including the Department of Defense.
> The head of the NSA is always an active enlisted officer who is part of the of the joint chiefs
No:
(1) The Director of the NSA is always an active commissioned officer (and a four-star flag officer during the tenure in the position.) Commissioned officers are not enlisted personnel.
(2) The Director of the NSA is not a member of the Joint Chiefs -- the Joint Chiefs of Staff include the Chairman and Vice Chairman of the Joint Chiefs, and the Chiefs of Staff of each service (Chief of Staff of the Army, Chief of Staff of the Air Force, Chief of Naval Operations, Commandant of the Marine Corps, and the Chief of the National Guard Bureau.) The Director of the NSA is Chief of the Cyber Security Service, but not every position with the word "Chief" in it in the military is a member of the Joint Chiefs of Staff.