That's just not true? South Korean ministers have been discussing building nuclear submarines domestically long before this current agreement.

And the US has an agreement with South Korea that limits domestic production of fissile material for military uses but it's a mutual agreement that we have with a bunch of countries (including China) and is essentially always renegotiable as situations change. Essentially it's just an explicit agreement of how much material a given country intends on producing for the purposes of requiring public political discussions domestically before ramping up production.

That is all very much a flexible situation and the US doesn't have any actual power to legitimately stop South Korea from manufacturing domestic nuclear reactors for military purposes.