No court is about to start issuing subpoena's to every BD out there. There is no legal cause to do so.
If a stock is trading it is near impossible to get data that is fluid daily without assurance that everybody reporting data reports for the exact same time after close. That is why it is best to be done during a trade halt and after all settlements are complete.
Since NOBO/OBO are likewise inaccurate in a fluid market and the "ex-clearing" hidden shares would be hidden from NOBO/OBO, you can't trust that. so....
If there are phantom shares in excess of Issued and Outstanding that shareholders are trying to prove, it requires account statements that prove share ownership in an account. That requires a law firm to operate as a trustee to this info and would require individual shareholders to fax in account statements that can be verified for authenticity showing the shares owned. Regardless of clearing issues or anything else, this is absolute. why you need to have the stock halted is that this takes a huge amount of time and will be entirely dependent on people reporting them in (highly unlikely),
Other than that, how else do you locate shares outside the system?
What is the issue you are trying to solve/prove and then match that up as to how the "normal" system works and see if what you intend to prove would be accomplished via natural channels. They generally don't when you are claiming fraud is taking place.