Certain E forms are not required to be certified by the professionals if they are filed by OPC, Small Companies and that includes INC-21 also (Notification dated 28.04.2014, Companies (Registration Offices and Fees) Amendment Rules, 2014. May be the authhorised capital of your company is less than 50 lac, therefore option is not activated to be signed by the professionals.
Stamp Duty can be paid manually or electronocally. If the amount of Stamp duty is too less, then you can purchase the stamp paper and attach with the form and fill the required details.