enigma1 - 2:46 pm on Aug 10, 2011 (gmt 0)
I'm seeing in Webmaster Tools, which says I have 40,000 duplicate title tags and description tags.
That implies somewhere in your domains duplicated pages exist or getting recreated somehow. I've seen it happening a lot with code that builds URLs accepting any parameter passed from requests (eg: pagination links generated from a search, carry all kinds of parameters and in many cases they just duplicate the ones from the request).
So when you put an item out of stock make sure it has completely dropped from all navigation elements if you want to do the 200 response.
If there is a single routine which generates the links (most carts work like that) - and there are no hard-coded links, you could deploy a log and check the caller functions to figure out the ones with the problem - if any.
Can you say more about the issues of leaving a lot of "out of stock" pages open for indexing?
I would think as the number of out of stock products increases and these pages remain exposed, so the site's info broadens and loses focus. Important links may now be hidden in the myriads of "out of stock" products and search engines may give priority to irrelevant pages. Your eshop should always keep focus of the important pages. The main navigation links (like a menu) do not always guarantee spider focus.
As I mentioned before depends what you carry. If I sell new items and I have a clearance section to get rid of returns, I would only expose to SEs one page/link for a clearance section/listing - of products and have the add-to-cart in the listing page instead of using a separate page.
If I sell only second hand items I would group the items by category or type etc. and focus SEO on the listing pages, if necessary I would use a js or a form for the product details page so customers can select fields and buy, but SEs cannot see them. Still items will be visible from the listings and should be indexed fast, as the page content would change often.