My main point is that people will get into the habit of using this, and will also use it in functions.
Clear is almost never needed in normal use, as you can use functions to keep your workspace clean. Close all should also be avoided, as you should use explicit handles to make your code robust. If there is an unexpected close all in a function, that will be annoying.
The big exception is during debugging. If you're using a script to quickly check something, these are fine. That is why all Image Analyst's demos start with it, and why you probably won't find any of them in his functions (with the possible exception of clc).