Will using the M.2_1 socket disable any SATA ports?

Yes — when the M.2_1 socket is operating in either SATA or PCIe mode, the SATA6G_5 and SATA6G_6 ports will be disabled. Additionally, when the M.2_2 slot is occupied by an M.2 device, the PCIe x16_1 slot will run at x8 mode instead of x16. You should plan your storage configuration accordingly before installing M.2 devices. (Page ix)