1: Can Trademark Agents empanelled with Registrar of Trademarks issue "Cease and Desist" notice ?
YES. He can issue the said notice.
2: Is it not necessary that for a third person to issue such notices on behalf of clients, he/she should be an Advocate?
Answer to the first question is a sufficient reply to this question also.
Que 3: Does Empanellement with various departements authorise such persons to issue outlandish Notices to other people?
It is not called Empanelment. It is Approved by. Empanelment is different from Approved. Therefore, your understanding is erroneous.
Que 4: Are such empanellements not meant only for prosecution on behalf of Clients with such departements only?
Answer to the question No.3 is a sufficient reply to this question also.
Que 5: If such Trademark Agents are not authorised, how should we deal with notices issued by them?
As it has been already stated that the notice issued by the Authorised Agent is valid, this question does not arise. The notice has to be dealt with and replied as though it is a legally valid notice.