"Does Tor still present a threat to the NSA?"
I believe that Tor was never threat to the NSA. There are several layers of 'protection' about Tor, thus several ways to attack users.
The first layer is: software code. NSA software developers can misuse open code to find holes and bugs in the code. We can surely make the presumption that the NSA doesn't have any problems to employ the best programmers to do the task. Inside of this first layer are also developers of Tor software. They don't hide; they educate the FBI, and they don't hide that they are financed by government entities, but say that they are independent in their work, no matter who finances them. I would add (layer 2): if Microsoft reported bugs to the NSA before they made patch/update, why do you think Tor developers didn't do the same? Remember the story about the Freedom Hosting server, and the fast Tor browser bundle update after the system administrator was arrested. FBI hacked the Firefox browser (or they got bug information from Tor developers) and snitched all users of the Freedom Hosting server. It means even users who just use anonymous tormail (that's not against the law).
Beside software, Firefox bugs are layer number 2.
The third layer is: servers, so-called Tor nodes. Even if software and Firefox are perfect, Tor nodes can spy on users. Besides intruding spies in such organizations who operate Tor nodes, stronger servers gather more traffic and it helps the FBI analyze traffic. Make a website to sell drugs/guns and collect thousands of users, and you will get a lot of traffic. So they will catch you fast.
4) The fourth layer is the PC. Microsoft, updates, antivirus software, all of them gather information from your personal computer and send it to different servers/companies. There are antivirus software that gather your links in the browser and send it for analysis to the producing company. Stupid example: When I want to visit movie servers, many sites are blocked as dangerous by Sophos antivirus software, so, corporations collaborate between themselves, and they can get information that I visit this or that website, together with my Mac and IP address. They can do the same when I use Tor software. So, if they want, they can hunt people on the basis of websites we visit.
Besides this, your PC can even have an installed keylogger or some more complicated spying software produced for the NSA, and the NSA makes a deal with antivirus companies to avoid detection by antivirus software.
I am not a professional, but I think users can protect themselves from developers and NSA with installing more and more private bridges and connect to them directly, to avoid public bridges and Tor nodes, But many people don't have money for that and they must rely on developers of the Tor network (who publicly cooperate with the US government).
So, many Tor users are exposed, if they use a website or they administer a website which is hunted by the NSA. And, yes, they can be arrested if the NSA really wants to arrest them. It depends on how much you come to their attention, and how important it is for them to hunt you.
Do you think people employed in data centers will refuse cooperation with the NSA? NSA can spy on every Tor node, with physical access to the server operating as a Tor node. When they attach a device for forensics to the server, or they install what they want in the server, they can spy without asking anything of the system administrator or owner of the server. And who knows how many nodes are even inside of U.S. Servers are the cheapest there, and many people will buy a server in the U.S. and many use Amazon S3 instances/servers to make Tor relays (Amazon, PayPal, and Visa/Mastercard. All of them are the right hand of NSA; just remember who sabotaged WikiLeaks).