The Dutch government making the decision to break its previously honored agreement with Japan was in exile at the time, and under the protection of those encouraging it to do so. A difficult position in which to say "no" to Washington and London.
A neutral Dutch government in control of its pre-war borders will not be in the same position, and may be persuaded to honor its previous commitments to Japan by a carrot-and-stick approach. The carrot would be Japan's ability to pay for continuing oil shipments in Chinese gold, and a possible Japanese guarantee of Dutch neutrality.
The stick would be German.
You might be right. Let's say for a moment that The Hague is considering ignoring the US demand for an embargo for the reasons you outline. What would be the Anglo-American response to that? Hull can still send his note, and would the Anglo-Americans consider occupying the NEI to physically prevent oil export to Japan?