Is supplier (operating under an ecommerce operator liable u/s 9(5)) exempt from GST in respect of non-ecommerce supplies also

No, in respect of supplies directly by such a supplier, GST registration, tax payment and all other compliances are applicable. However, for purposes of threshold benefit, supplies through ecommerce operator would not be included.

(ICAI FAQ PUBLICATION 06-09-2017 REVERSE CHARGE: FAQ NO. 49)