For me, the pages in this Supplemental Index indicate many things and they are not all bad. In fact, I think many of those pages in the SI are only there temporarily. For those of you watching daily, this must be stressful, eh? ;)
The reason they are there? I can't give you an official reason but here is my "bottom line take" on it...
They just don't have enough PR to make it into the primary indices, bottom line.
Old pages being recaculated. New pages being calculated, yada, yada, yada. It's an ongoing "by the second" process for Google 24/7/366.
Remember when we had monthly updates? Then bi-monthly? Then weekly? Then daily? And now by the minute in some instances. When I talk with clients, I refer to Google's index as a "Rolling Index". It is in constant flux. Can you imagine the sheer number of pages being crunched across all those datacenters?
What used to be the official SI no longer exists from my perspective. Googles indexing patterns have evolved to a point where that SI has a different meaning than it did previously. It's more of a holding area for pages it doesn't exactly know what to do with.
All sites are going to have a certain percentage of their pages in Google's "Rolling Index", it is a given. You cannot expect every single page of your site to perform, that just isn't going to happen unless you have just a few pages. ;)
Do you have the potential for generating 100,000 product pages? I'd expect you to see at least half of those in this "Rolling Index" at any given time. If the site is dynamic and things are changing, there is constant recalculation going on which means movement amongst the indices. And, just because they appear in this SI, doesn't mean they are not performing, does it?
No, the real metric here is what is happening at the analytics level. Out of those 100,000 pages, which ones are not performing? I'd be willing to bet that many of them are at deeper levels in the click path and just haven't been able to establish themselves yet. Change the click path. Point some external links to the level above in the click path. Change the indexing pattern of those pages that are not performing. All that can be done by changing the click path. "Roll your content". :)