If you were publishing each of those to a folder and then uploading to your iDisk then it would disable/remove the counter. You can publish directly to .Mac from iWebSites but, as you probably already know, the last published site will be deleted.
If you have all of our sites in one domain file and have edited only one, that's the only one that should be uploaded. Move it to the top of the list in the sites pane and use the Publish to .Mac menu option. The counter should work. But you may have to do a one time Publish All after getting all the sites in one domain file.
If you use Statcounter you could publish to a folder and upload. But after each publish, you'd have to post publish edit the page with the statcounter to add the code again. It's not very difficult if you put in a text placeholder and then find that placeholder text and replace it with the code. I've go a file with the code for each of my sites using statcounter so I can just cut and paste.
Not really as I've been told. The snippets code go into a different file and are called up from there. I remember it being stated in a post that unless the code is in the actual file that's being counted it won't work. I haven't tried it out to see it that's the way it works.