less,
1. Kitniyos contained in a box of processed food that has reliable hashgacha that it contains no chametz. Why is that assur?
For the same reason that Ashkenazim do not triple-check and eat rice on Pesach. The Poskim chose to restrict consumption of these foods and their derivatives, rather than permit them to be consumed with careful checking. Aside from the Beis Yosef, whom Sefardim rely upon.
2. Are peanuts , beans or mustard seeds ground into flour or grown near chametz? If not, why are they kitniyos?
They most certainly were and in many cases still are. In addition to these two reasons, the Ba’al HaTanya added that kitniyos, when cooked, is very similar in appearance to the five grains when cooked. Which is a reason why corn is considered to be kitniyos, yet according to the overwhelming majority of opinions, potatoes are not.