Police can ask only the information that is needed only by due process of law. And not because it feels like asking for information.
There are many points of law involved related to fundamental rights of not only the trading company but also individual fundamental rights of the employees. What is the purpose of collecting information by Government? Is it for administrative, policy making or planning? If yes then required data under Census Act is already available.
If the company has done some offense it does not mean each and every employee is also complicit in that offense. If any personal or private data of any employee is disclosed without authority of law, then those employees may also file case against the company.
Had any cognizable offense taken place then Police would have already arrested the accused and seized the connected property/ information with the alleged offense. Either it is non cognizable offense or no offense at all and are doing fishing expedition to ferret out suspects.
Therefore it is important to know under which provision of law information is being demanded. Accordingly if required, matter can be taken up in Hon'ble High Court for relief.