When I first read your observation, I freaked just a little because there are a few internal pages where I struggled for a long time to get them to rank instead of the home page. Fortunately for those sites, those internal pages I worked so hard on are still ranking for their longer tail phrases and I'm not seeing any effect like you mentioned.
Maybe someone else has noticed it in their niche, however. It is the kind of thing that has tended to see-saw quite a bit.
Google's Panda change was big and it looks like they have some other changes that are smaller but still significant over the last few months. I have not seen any significant problem with long tail keywords and deep content. My network of sites is still generating good traffic for deep pages.
One Panda theory (or perhaps one of the other recent Google algorithm tweaks) is a devaluing of internal linking - which would be expressed as favoring pages with stronger external backlink profiles, most typically gains by home pages.
As what has moved up in many long tail searches are home pages.
I've seen this on my site and I was not hit too hard by the Panda updates.
Pre-Panda, I noticed that when I did an internal navigation change (major site change), Google would replace the ranking internal pages with the homepage. Then after a trial period, the internal page returned.
I am wondering if one of the effects of Panda is that Google is replacing internal pages with home pages as it re-assesses the value of the internal page.
I've noticed the overall bounce rate of effected sites has improved in the last month by 2-5% . Strange that it would be consistant. It's the first time I've seen improvements in line which so directly relate to teh long tail / deeper queries.
One of my sites clearly had some sections that gained a lot with the launch of panda. We have four main types of pages on the site:
1) Homepage and top level pages that are designed to rank well for competitive one or two word phrases. 2) Local pages for cities in the US advertising a listing of products in our niche that are available in that city. 3) Articles about our niche (several hundred) 4) Profile pages for our users (tens of thousands). We require each user to write at least a paragraph about themselves.
1 & 2 attract highly qualified search engine traffic that is easy to monetize. Types 3 & 4 attract less qualified tail traffic.
Post panda, traffic to 1 & 2 has remained fairly constant. Traffic to 3 & 4 has tripled.
This hasn't helped our bottom line as the profile pages especially are not great landing pages.