Either the data or system is secure, or it isn't. Technologically, if there is a way for a judge to authorize reading a single X; then it is a hole that eventually will allow to read all X without the warrant by others as well.
As an example, if a cellphone network software allows for FBI wiretaps, then that can be used also by illegal wiretapping (http://en.wikipedia.org/wiki/Greek_wiretapping_case_2004%E2%... - the criminals weren't even identified). And if a system is secure (for any reasonable definition of the word secure), then noone can break that security, no matter what warrants they have.
There is no middle way. If I'm allowed to protect my communications from random illegal snoopers (say, corporate espionage); then that protection will be just as effective against legal snoopers.
2) There are freely available steganography/hidden volume tools that make it impossible to verify IF there is something encrypted - for example, you might guess that a hidden volume exists, the accused may decrypt N hidden volumes, but noone would be able to check if there is another N+1'st volume for which a key was not provided.
Well, the alternative is that the government has access to everything, all the time, and we just have to trust that they're not going to misuse it.
Also, your wording implies that if a government agency does have a valid warrant, that this means they're somehow entitled to whatever information they seek (within the parameters of said warrant). This is patently absurd to me. If the government seizes an encrypted document with a valid warrant, more power to 'em. Have fun brute-forcing it. Doesn't mean I owe them the passphrase.
I wasn't suggesting entitlement so much as practicality. Up until recently, the distinction you're talking about didn't really exist. A warrant might not give police an "entitlement" to something in your house, but there wasn't really a lot you could do stop them from getting it. The best you could do is hide it which isn't very practical in a lot of situations.
But with an encrypted document, suddenly you have new protections. As you suggest, a warrant does the police no good because you also have the right (under the 5th amendment) not to tell them how to access it. Unlike a safe, forcing open an encrypted file might turn out to be impossible. Now you have a technical protection against searches that goes way beyond the legal one found in the 4th amendment.
Again, I'm not saying this is a bad thing, but I think it's an interesting way to look at it and at least one of the points I saw in the article. Technology is less a means to ensure 4th amendment rights and more a means to go beyond them...for both good and bad reasons.
Now I, as a (hopefully) rational human being, have a choice again.
I think this may have been the point of the article's title (aside from being attention grabbing). The 4th amendment gives Americans the right against unreasonable searches without a warrant, and some similar legal protections exist in many other countries. But the technology the author is discussing generally has a design goal of preventing all searches, under any circumstances. In other words, to technologically ensure a right you never possessed in the legal sense. It provides protection for people and in situations not even the most rights respecting government would be likely to legally protect.
This doesn't make the technology bad, but it's a very interesting thing to think about, which is what I suspect was one of the points of the article. For better or worse, technological protection has the potential to go well beyond legal protections.