The Constitution states, 'no Bill of Attainder or ex post facto Law shall be passed'; to the extent that those executive agencies' enabling legislation permits ex post facto regulations, that legislation is unconstitutional.

They're definitely not. They've resisted due process for some time. NSA's reps even argued in Jewel case that judicial branch shouldn't be allowed involvement at all. Which is sort of the status quo for intelligence agencies and courts. Prosecutors similarly have a combo of broad powers, immunity in common abuses, and virtually no accountability. The government as it exists certainly doesn't run in the framework of the Constitution except in a partial way.