Does the net value of taxable supplies include all the transactions made through electronic commerce

No, net value does not include transactions pertaining to supply of services notified by the Government under section 9(5) of the CGST Act, 2017. Net value of taxable supplies is the aggregate value of taxable supplies of goods or services or both, other than services notified under section 9(5) of the CGST Act, 2017, made during any month by all registered taxable persons through the operator reduced by the aggregate value of taxable supplies returned to the suppliers during the said month.

(ICAI FAQ PUBLICATIONS 06-09-2017 TAX PAYMENTS, INTEREST, PENALTIES AND OTHER AMOUNTS: FAQ NO. 50)