This will happen with GUIs as well, once computer-use agents start getting good. Why bother providing an API, when people can just direct their agent to click around inside the app? Trillions of matmuls to accomplish the same result as one HTTP request. It will be glorious. (I am only half joking...)
Half joking, sure, but the "click around the app" problem is already real for teams running browser automation at scale. The issue isn't the clicks themselves - it's that every Chrome instance looks identical to a bot detector the moment you spin up ten of them from the same machine. The fingerprint (canvas, WebGL, navigator properties, etc.) is basically screaming "I'm automated". Dealing with this from the ops side: the headache isn't writing the automation, it's keeping each browser session isolated enough that sites don't treat them as the same entity. MCP or CLI doesn't really change that underlying problem.