Is it permissible to pay Zakat from the funds of an orphanage company that have not yet been distributed, before their distribution?

If your nephews are adults and mature, they are free to dispose of their money either by keeping the company or dissolving it. They are obligated to pay zakat (definition) on their shares if they reach the nisab (definition). However, if they are under your guardianship and have not reached maturity, you must manage their money in a way that serves their best interest, and pay zakat on the money of whoever's share has reached the nisab and a full year has passed over it. This is the view of the majority of scholars.