If you're skirting KYC requirements on the basis of this belief, you should seek legal counsel.
A business is considered to be a type of entity (just like a person) that gets different tax treatment.
Anyone who transfers money, by any manner including, but not limited to, electronic, financial, debt ledger, cash or traditional methods like hawala, hundi, fei ch'ien, and chit is considered to be a "Money Transmitter."
Money Transmission classification and registration varies by state, to receive money from, or transfer money to someone in said state (regardless of your jurisdiction) you must register with the state and usually put up an insurance bond.
Then you must also register with FinCEN and enact an appropriate AML policy that would include KYC.
Non-profit status is given by the IRS, allowing the entity to avoid taxes. It doesn't change the underlying entity's structure.
NB: I'm not a lawyer.
KYC is regulated by FinCEN. FinCEN requires every “Money Services Business” to register with them and do KYC.
If maintaining a supernode is so costly that only businesses will do so, to make a profit, then supernodes might require KYC. If supernodes run non-profit, they don’t need to.