Certain MP3 files not recognized in iTunes

I have found many .mp3's that are in my music folder (on hard drive) but NOT in my iTunes library, dispite the fact that they were all manually added to the library at the same time. This may seem trivial, but when you have over 30,000 songs, it's hard to know which ones are not shown in iTunes.
I've noticed that the ID3 tags in some of these songs are only using Version 2 ID3 tags and not also using version 1. When I update the tag (using WinAmp) to include both v1 and v2 the songs are automatically recognized by iTunes. One might sumize that iTunes requires ID3v1, but I have many, many songs without v1 tags that are recognized fine.
Any ideas why iTunes doesn't recognize these songs and what I can do to figure out which of the 30,000+ .mp3 files needs to be updated??

First, iTunes' default settings are for it to copy music to the iTunes folder structure when you add them (but leave the original in place, although it no longer refers to it), and for iTunes to manage your music for you in a very specific folder structure.
Second, the listing you see in iTunes is not generated by iTunes directly referring to your files.  It keeps a library database of the files you have added and in those listings it keeps all the information about that track, including its location on your drive. When you play a track, iTunes uses that listing to go find the media file and play it.
If you do any file renaming, manually deleting, or moving of files and folders, or anything to break that link between where iTunes' library thinks your file is and where it actually is (or was, if you deleted it), you get "!"
You say you are able to play them but iTunes cannot find them.  It would help to know how you are playing them if iTunes cannot find them.  Are you playing them in Quicktime?  Also, you say you see the files, but are they in the iTunes folder structure (assuming you use default settings), or are these the originals?

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