Yes, I've heard similar reports. But the problem, as you may know, is that we have no certainty about the Supplemental Index anymore. To compound that, Google spokespeople have said they were continuing to make changes and upgrades to it. We're rapidly going into the region of having no dependable information.
I'm currently working with a site that shows 10 urls that are PR5 to PR7 - what can I make of that? My advice for now is not to try anything based on the current reporting tools, whether the official ones or the * hack for the site: operator that you mentioned. Google's reporting features and operators are way too volatile for my taste at this moment. I don't like to take actions on suspect data.
If you are seeing new ranking problems appear, and not just perceived "supplemental index" problems, then you may want to experiment with nofollow to unimportant pages. However, I'm not a fan of that approach either, although I do recognize that some people feel it has helped them. As I see it, many webmasters became terrified of the Supplemental Index because in the beginning around Big Daddy, its implementation was buggy. And now, that traumatic memory continues to get people upset and spend time in needless attempted manipulations - sometimes hurting their traffic.
I would rather let Google do whatever Google is doing with supplementals. We are too much in the dark to try to "help them out". There's nothing wrong with feeding some link love to pages that aren't ranking well, and removing juice from urls that don't really matter -- but it's ranking that counts, not whether the url is apparently in the supplemental index.
That said, I agree that seeing so many urls leave the main index is troubling. It may well be a sign that something's wrong. But again, what does your actual search traffic look like? That is the real key, and not the way Google chooses to partition their data.
Are you sure that you've eliminated multiple urls pointing to the same content? Have you used unique titles and meta descriptions throughout all your important content? Have you addressed any thin content pages? Madesure that extensieve boilerplate copy does not appear on many pages? I would definitely address all of that before going down the nofollow route.
If you have many links pointing to those link index pages, and from many different urls, maybe tone that number way down.