I found this as well, in addition, it removed an entire folder that I had in my iDisk folder that was in the directory structure for iWeb, but wasn't put there by iWeb. This one pissed me off. (In the past, when I posted pictures to MacRumors, I would link to them as they sit on my website, not attach them, those pictures are now all gone.)
What the OP is specifically complaining about is that before, iWeb sites were stored on your iDisk in: /Web/Sites/iWeb/<sitename> now they are in just /Web/Sites/<sitename>
For example, my site is named "[deadsite]", so it was /Web/Sites/iWeb/[deadsite] and it is now /Web/Sites/[deadsite]. Which means the URL has changed from "
http://web.mac.com/[dead]/iWeb/[deadsite]" to "
http://web.mac.com/[dead]/[deadsite]" Which means... If I had my iWeb site's URL posted anywhere, I have to go change it.
For intra-site links, though, you should have been using relative links, not absolute links, anyway. (So that a link inside your site should be to "../Images/myimage.png" rather than "
http://web.mac.com/moistproductions/iWeb/moistproductions/Images/myimage.png") Not only will it survive moving the website more nicely, but if you change all the links to shorter relative links, you can save a decent amount of file space.
While I do appreciate the simpler URLs (and more readable now that they are missing spaces/%20s,) it would have been nice if they had made some kind of automatic redirection from old style to new style on .Mac's end. (And, more importantly to me, didn't go deleting manually created folders!)