What if they had to subpoena a tomato grown in a field next to the toxic waste dump? What if they opted not to examine that tomato because they didn't have the resources to issue, process, and support, the lengthy bureaucratic process involved in such things?
But the government can and should have the right to inspect a tomato (not necessarily a specific tomato) if all the tomatoes in that field are slated to go direct to consumers, right?
Similarly, what about testing for drug quality? You could even extrapolate it out to the SEC's right to examine a private financial transaction in order to determine legality. Or the IRS's right to inspect one's taxes to determine compliance.
Point is (IMO) there is a need put on government by society to bypass some of our "Inalienable" rights. In most cases this societal decision is necessary and makes sense, and I'm arguing that code inspection of life-critical systems is a reasonable example of such a case.
To extend the metaphor, if the farm that grew the tomato is selling them to people to eat, I don't see that a subpoena is or should be required. But it breaks down anyway, because a tomato's source code is right there in it, with no opaque binary blobs to worry about trying to decompile.