The reason I never noticed the increasing subordination of google reader (a product I use daily, or even hourly), is because I have other shortcuts for products I use that frequently. In fact, it's a little strange to me that someone would go to the google homepage in order to navigate to reader through the nav menu. That would never even occur to me. If I was already in the location bar, I would simply type in the url for google reader. Why would you type in the url for google homepage instead?
I think there are more people who have their browser's home page set to google.com, where every new window or tab opens that page automatically. When that's the case, why have bookmarks for other Google properties when they're already available on your default page?
Granted, I'm in the minority of users who set their homepage to "about:blank" so that it's up and ready as fast as possible and focuses the location/search bar by default. I use bookmarks to open new tabs for just about anything I visit on a regular basis.