A variation of the threat very much exists: Do you know (meaning, there are no unknown unknowns) that no piece, anywhere in your toolchain (OS, compiler, library, framework, buildtool, CI etc), contains malicious code? At the time Thompson made this comment, he talked about the C compiler because it was the one bit of shared code everything else depended on. Today, the attack surface is much, much larger. If I was ru…
Sure, but it sounds like you're talking about a standard hidden backdoor. This is a pretty straightforward and obvious threat. What Thompson describes is a whole lot more devious and difficult to detect.
Thompson's scenario is more devious, more difficult to detect, and a lot, lot harder to implements (near impossible, as some of the SO answers point out). But at that time, people didn't generally download millions of lines of code written by perfect strangers and incorporate them into their programs, so that was the only way to pull such a thing off.