While for the most part I agree with you, there are sometimes when it seems... appropriate. Take, for example, Google Docs. I'm used to hitting CTRL-S when working on just about any paper. If I had the save website dialog pop up every time I hit CTRL-S, I would start to get annoyed. I'm glad that Google Docs doesn't do that. A similar case can be made here.
I wonder if the shortcut should be removed. Certainly some people use the feature, but it seems obscure enough that maybe we should pass that combination on to the website, instead.
Though you get an html file and a folder with all the external assets, which I find to be pretty annoying. Safari did a single .webarchive file, but I don't think anyone else ever standardized on something like that.
It often wrecks the layout, but I tend to print to PDF rather than deal with saved html files.
Save-As writing bunch of resources, that when loaded back into the browser might even be broken by lack of external resources are also, in my oppinion, a bad way to keep evidence (e.g. CYA). If you need it to persuade a non-computer-savvy person of something stated on a website, I'd say a bunch of random files in a directory is also much less convincing than a "printed-to" pdf, or screenshots you can easily mail around.
Regarding the .webarchive, I think IE supports another type of "web archive", with a .mht ending.
