Matts says that this query attempts to estimate the numbers of pages that are in the Google index for the domain but it is never a complete or exact amount.
Google shows results to three significant digits of precision. For example when I did a query for site:ineedhits.com it generate “About 1,080 results”. Matt also mentioned that a query for the yahoo.com domain will return about 138,000,000 results. By only showing results to three digits, this allows Google to give you a quite accurate idea of the results, but they don’t ever claim that these are exact amounts.
Matt suggests that usually when you get past a few thousand pages in the index, then the results aren’t as relevant or useful. You should more be concentrating on the traffic you are getting to your pages and there return on investment.
So, now you know there is no need to worry that all your pages aren’t being indexed by Google. Chances are they are, but Google just isn’t showing the exact results.