From what information is out there, it seems like the most likely scenario was that the US Government wanted these companies to install back-door technology into their systems and give the government agencies access to all the information that flows through them; these companies would be ordered to not disclose the backdoor nor the government's involvement.
This appears to have happened back in 2007 with Hushmail. Faced with such an order, the company's only option is to either quietly comply or cease to exist. Note that Hushmail is a Canadian company, but it was nonetheless forced to comply with the US order.
Why is email the only aspect most vendors are concerned about?
Here's what Silent Circle said:
There are far too many leaks of information and metadata intrinsically in the email protocols themselves. Email as we know it with SMTP, POP3, and IMAP cannot be secure.... And yet, many people wanted it.... However, we have reconsidered this position. We've been thinking about this for some time, whether it was a good idea at all. Yesterday, another secure email provider, Lavabit, shut down their system less they "be complicit in crimes against the American people." We see the writing on the wall, and we have decided that it is best for us to shut down Silent Mail. We have not received subpoenas, warrants, security letters, or anything else by any government, and this is why we are acting now.
In other words, they didn't think offering the illusion of secure email was particularly useful in the first place because significant data leakage is inevitable in the associated protocols.
But more importantly, once you receive a government order, you no longer have any choice. At that point it becomes too late to stop offering your email service as the order will prohibit you from doing so. At that point, you you must continue to offer your service and pretend that it hasn't been compromised. Otherwise you have to cease all operations altogether.
Silent Circle is hoping that by closing down their email service, they'll be less of a target for spying agencies and will avoid being ordered to compromise their services.
Is any certificate vendor, like Verisign, that issues S/MIME certificates susceptible to government subpoena?
What about non US companies?
In many cases, yes. There are a few nations where a US order can't be enforced, though these probably will have their own governmental interference to contend with.
What expectation of privacy should I have when doing business with any US vendor?
Not much. Though to be fair, other governments do similar things as well. Which means realistically, you have no expectation of privacy that you cannot actually prove yourself.
Does my citizen status matter, or does it matter if I'm in the US or not?
The NSA explicitly asserts that all communication anywhere in the world that involves at least one non-US citizen is theirs to collect without cause. They also state that information that they can't prove involves only US citizens will also be collected just in case. The NSA and FBI also have largely unlimited power to force US residents to comply with nearly any surveillance order if they can get a sign-off from a court. That power largely extends to any other nation with which they have a legal assistance treaty, which covers a lot of ground.