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If the charities are beneficiaries of the trust, and this is not merely a donation, then a K-1 beneficiary form is filled out with the payment to the charity. It does not mean the charity pays taxes, it is just a designation from the trust regarding a payment to beneficiary and the charity in this case is indeed a beneficiary. Since the charity is a non-profit, when they get the K-1 it does not mean anything, since they do not pay taxes on the amount.
You do not pay tax on the amount donated to them from the trust, as they are a named beneficiary they get their share and the K-1 to show it went where it was supposed to go.