Is it permissible to use the kunya "Abu Malik and Al-Layth" instead of just "Abu Malik," and is there a precedent for such a kunya?

Assuming a kunya (patronymic/teknonym) is from the Sunnah and good customs. It has been a common practice for the kunya to be by the eldest child, but there is no harm in it being by someone other than the eldest or by someone other than one's children, as the matter is broad. Indeed, some of the Salaf had more than one kunya. For example, Uthman ibn Affan was known as Abu Abdullah and Abu Amr, and Ali ibn Abi Talib was known as Abu al-Hasan and Abu Turab.