Let me put my two cents on it.
First, on how to treat the absence on account of Bandh... I do not think there is any law in India which states that General Bandhs are illegal. They are part of the constitutional right of expression, and therefore, no court interferes and awards injunctions against this Bandh. There are laws pertaining to strikes in industrial establishments but not governing bandhs called by political parties. There are advisories issued by the court, but in law, there is no provision that prevents it except ESMA. Strikes are considered an inherent right; therefore, there is a provision for strikes under the ID Act and Standing Order Act.
Having said that, we need not just look at the legal side of this. As mentioned earlier by many speakers, we need to consider the social situation/environment. Safety and security are of prime concern, and we all know the risks associated with it. Despite their best efforts, ruling governments and law enforcement bodies could not maintain normal services in any city. Expecting employees to risk their lives for that day's work is the organization's decision. Organizations have to decide what view they want to take on this. HR leaders are the main influencers in this. So each one has to ask oneself, what's their personal answer.
The majority of people/organizations also understand the economic loss it brings to the organization, and employees cannot be free from that; therefore, they have to cooperate and work towards recovering from this loss. With that spirit, most employees/organizations work an additional shift/another day (weekend, etc.) to compensate for this joint loss.
On the issue of the Negotiable Instruments Act... I do not think this act deals with any holiday; it only regulates how the holidays should be treated in financial terms. That is, if that was the last date for any financial commitment, the date will be extended accordingly, and there should not be any penalty or be treated as defaulting on the commitment.
It is the role of HR to educate and get leaders of the organization to understand this and make decisions accordingly.