S.M.A.R.T. monitoring can only be disabled from the system BIOS. S.M.A.R.T. remains enabled on the drive. If S.M.A.R.T. is disabled from the system BIOS it will not poll the hard drive for S.M.A.R.T. attributes during system startup.
If you cannot find the S.M.A.R.T. option in the system BIOS please consult your system manufacturer or manual.