It's actually the inverse. Tax doesn't apply to the interchange fees, but interchange fees apply to the tax. In other words, the interchange fee, or the merchant fee that gets charged to the merchant, applies to the entire transaction, which does include tax if it's a taxable purchase, or the purchase might be a non-taxable purchase, in which case the interchange fee just applies to the total amount of the transaction.
The interchange fee applies to the transaction amount, which may or may not include tax, but the interchange fee itself is not a service that's subject to GST.