At least the cookie jar is half full! I personally would commend them on their self-control and not finishing all the home-made cookies, which I sure are delicious (and nutritious). However, there is the aspect of educating them to obey your reasonable requests and teach them to show discipline and respect for parental authority without disrupting family harmony.
If you ask them outright there is a mitzvah of honoring one’s parents, which would compel the eater to confess or the sibling to tattle, depending on which child you ask. If you ask them both at once, “Who ate the cookies?” the eater would need to confess and the sibling would need to deny guilt, implying who the real culprit is, even without pointing his finger (the Chofetz Chaim writes that when the wrong person is being accused it is better to phrase the denial in such a way that it is not pointing a finger at the other person. Rather, it is better to say something that makes it clear that he wasn't the guilty party without saying directly who actually did it).
I think it’s most likely that they both had a hand in the jar unless one had near super-human control to refrain while the sibling enjoyedthe treat.
Only you, as their mother who knows their natures, could really evaluate if this direct approach would help them be more well-behaved in the future, or if it would – on the other hand - cause embarrassment, resentment and self-esteem issues going forwards.
Perhaps it would be better to tell them how you are disappointed about what happened and how you expected more moral behavior from the children you love so much. Tell them that instead of disobeying you they should feel free to discuss anything with you openly and without fear – including about permission to have a few cookies before dinner even after you said no. Explain that you want only what is best for them and will always be there to help, support and love them. That is the message I would suggest you try to convey in your own way, and I wish you and you husband much happiness and success in raising your children to the values of truth and kindness that we have “inherited” from Abraham and Sarah and the rest of our illustrious and beloved ancestors.
