A product that I am working on collects several thousand readings a day and stores them as 64k binary files on a NTFS partition (Windows XP). After a year in production the
Aside from placing the files in sub-directories..
Personally, I would develop an application that keeps the interface to that folder the same, ie all files are displayed as being individual files. Then in the application background actually takes these files and combine them into a larger files(and since the sizes are always 64k getting the data you need should be relatively easy) To get rid of the mess you have.
So you can still make it easy for them to access the files they want, but also lets you have more control how everything is structured.