You should understand that it is a "Digital Contract", which is nothing but a "Contract" in the first place. So, The Limitation Act, 1963, will be applicable unless and otherwise overridden.

As per Limitation Act, the limitation is 3 years. But having said that, the court will not allow you to sleep for 3 years and come and raise a dispute on the last day. By saying reasonable time, it means that you raise a dispute as early as possible, but the maximum time limit is 3 years. After this 3 years, your petition will not be entertained. Within 3 years, you can raise a dispute, provided you give valid reason for the delay.

Say you raise a dispute after 2 months, the court might ask as to why the delay of 2 months when you had received the mail earlier. You can justify this delay and say that you were abroad etc. or that you tried to resolve it with the agent for which you can show some mail exchanges etc. then it becomes a reasonable ground for condonation of delay.

I agree that Indian Laws (for that matter every other country laws) are not fool proof. But these simple things as far as limitation is conscerned are definitely taken care of.

If you if you do not dispute the contract note it is deemed to be accepted by you 

2) reasonable time is not clarified  in section 12 IT act 

Please go through Sec.10 A which will prevail all other rules. Don't confuse with the time limit, simplicity in this is that if the contract is specific and is not against the contract law then if no objections raised then it has been accepted. 

A notice / reminder can  be given to the SEBi regarding acknowledgement citing that if no acknowledgement or disute is given then under SEBI law you shall understand that it accepted as not disputed. Sir reasonable time in each case has to be seen on merits it depends on facts and circumstances of the case not whims and fancies. 

See it is left for the interpretations and same in your case can be deduced from time of contract. As to confirm reasonable time you can always seek acknowledgement by giving an reminder.

You have to dispute contract notes within reasonable time and it cannot be disputed after considerable length of time 

They usually put it on their website available for download. You might have to search for the same.

Yes.