One possible situation may have be that the missing songs were deleted or moved, which would cause iTunes to not know where they went. Best way to check on this is to find one of the songs that iTunes can't find anymore, right click on the song and select "Show in Windows Explorer". The file location can also be found by right clicking and selecting "Get Info" -- it's listed at the bottom of the Summary tab.
When you add files to your library, all iTunes does is create a short cut to that file in the "Media Library". It does not copy it to a single directory. It's important to understand that iTunes merely catalogues your music, rather then manages it.
That said, you can change that. In iTunes preferences, under the "Advanced" tab there are two options that just about everyone should have checked (by default, they are not). They are "Keep iTunes music folder organized" and "Copy files to iTunes Music folder...".
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