The issue is that the subpoena told Twitter/X not to inform the accountholder that their information was going to be given to the NYPD, nor inform the accountholder of the subpoena's existence. While that's enforceable with a warrant, it is not enforceable with a subpoena.
This shows how NYPD is attempting to compel companies to provide them with personal information of users, and keep it secret from the users, all without needing a judge's approval or warrant. That is not the proper channel to do this, and they know they have no legal leg to stand on which is why they aren't going to try to fight it's legitimacy in court.
When presented with an administrative subpoena not backed by a warrant you may be able to deny the subpoena without being guilty of such crimes.
However it does look like this is different from the normal subpoena process. This doesn't seem to be part of discovery - there is no action. The referenced "Section 14-137 of the New York City Administrative Code" seems to basically grant the NYPD commissioner powers a judge usually has. So there is something to worry about.
Having been the victim of these on many occasions, I can also see the original article seems to have things slightly twisted. The SCA gives the power to any governmental body to subpoena metadata from providers under an administrative subpoena without notice to the user. 18 U.S. Code § 2703(c)(2) I think.
It's the content of records that starts to get into constitutional areas such as 4th Amend. requirements.
The third-party doctrine muddies this under current law.
I don't understand why Rabbi Copwatch would be involved in fighting the subpoena.
Rabbi Copwatch should sue NYPD for infringing his civil rights by spying on him.
He has nothing to defend against. Under current law, if he doesn't want NYPD siezing papers and effects about him from Twitter, that is not his papers and effects, he needs to stop giving copies of data about himself to Twitter. I don't like that law, but I think that's where the law sits today.