You can doubt that a state sponsor can hide its authorship of terrorism if, and only if, you assume that American counterintelligence is omniscient. I do not make that assessment of U.S. counterintelligence, and perhaps that is where we differ on the issue of state-sponsored terrorism.
May I also suggest that your confidence in the media is misplaced? You say "I'm convinced—by my friends in the intelligence world and the accounts not just in the NewYork Times but also in the Los Angeles Times, Newsweek, and elsewhere—that the source of the al-Ani/Atta story recanted." The New York Times story, as I already pointed out, was based on a fabrication. The Newsweek story of April 28, 2002, did report that "the Czechs quietly acknowledged that they may have been mistaken about the whole thing." That version was repeated in other newspapers, including the L.A. Times. However, on May 3, in response to those stories, the interior minister, Stanislav Gross, called an extraordinary press conference and stated, "I draw on the Security Information Service information, and I see no reason why I should not believe it." As far as anyone recanting, Gross said he had consulted with the chief of the counterintelligence service, Jiri Ruzek, on May 2 in order to find out whether the Czech intelligence service had any new information that would cast doubt on the meeting. "The answer was that they did not. Therefore, I consider the matter closed." So the Czech government did not recant, nor did its source recant. Don't be confused on this issue by the fog of journalism generated by its persistent clip files.
As for the CIA, Director George Tenet testified June 18 before the Joint Inquiry Into Terrorists Attacks: "Atta allegedly traveled outside the U.S. in early April 2001 to meet with an Iraqi intelligence officer in Prague; we are still working to confirm or deny this allegation. It is possible that Atta traveled under an unknown alias since we have been unable to establish that Atta left the U.S. or entered Europe in April 2001 under his true name or any known aliases." That is hardly a denial: It is a report of an investigation in progress, and, as you know from the botched investigation of the first World Trade Center attack, such determinations take time. I suggest that before rushing to judgment based on flawed media reports, you might wait until the CIA completes its investigation, even if that requires interviewing Consul al-Ani in Baghdad.
But let's get beyond Prague and go to your central point: "a paradigm shift had taken place—that the real terrorist threat came increasingly from 'non-state actors,' not from states." Here we disagree. I submit that state sponsors always have been, and remain, crucially important to terrorist organizations.
States, and only states, have embassy bases in which their officers are protected by diplomatic immunity, diplomatic pouches, and courier planes (which by treaty cannot be searched for weapons), consulates (which can issue travel documents to agents), secure enciphering of communications, and state banks (which can transfer virtually untraceable money to the accounts of operatives). They also have internal security services to threaten and compromise relatives of prospective agents. No free-lance group has such resources.
Let us not forget that al-Qaida was a state-supported organization from its inception. When it (or its precursor) acted as an anti-Soviet mujahideen group in Afghanistan, it was backed by the United States, Pakistan, and Saudi Arabia. After it broke with Saudi Arabia over the first Gulf War against Iraq, it was backed and quartered by the Sudanese government. After the U.S. Embassy bombings in 1998, it moved to Afghanistan where it received safe haven from the Taliban government, which was in turn backed by Pakistan and its intelligence service, ISI. It was because it had safe haven in Afghanistan that it could organize its operations. After the U.S. government and Pakistan deprived it of this state support in November 2001, it has not been able to organize a single successful attack in America.
Other jihadist terrorist organizations, despite their nominal independence, could not exist without state sponsorship. For example, Harakat-ul-Ansar in Kashmir depended almost entirely on Pakistan and its ISI training camps in Afghanistan. Yet on the State Department list that you refer to, Pakistan was not included among the seven state sponsors of terrorism. The relationship between state sponsors and your "non-state actors" often involves murky, and temporary, marriages of convenience. Yossef Bodansky, the former director of the Congressional Task Force on Terrorism and Unconventional Warfare, wrote in his 1999 book on Bin Laden that "terrorist operations in several parts of the world now attributed to bin Laden were actually state-sponsored operations."
True, as you point out, "non-state actors" have become increasingly important, but, in my view, it is a mistake to assume they are necessarily isolated phenomena. Some may be acting alone, and some may have covert backing from hostile states. After all, isn't camouflage the true art of the state?
It is in this context that I deem it worth pursuing the investigation into whether or not the perpetrators of 9/11 had state support.