There is currently no way to hide files depending upon their extension, but I'll add that to the suggestion list. ioFTPD does hide any file that starts with .ioftpd so it can hide it's own permission file and a number of exec based scripts take advantage of this with filenames for their use like .ioftpd.lock, etc.
ioFTPD also hides any file/directory that is marked by windows as a hidden file. This hides thinks like Thumbs.db, Folder.jpg, as well as important directories like the Recycle bin, System Information, etc if you've shared the root folder of a drive (that is NOT recommended).
If no user (including master accounts) should see the file you could just tag them as hidden in windows. This means you won't see them in explorer unless you have Show Hidden Files/Folders enabled in windows. I know ioFTPD correctly handles the expected hidden files like thumbs.db but it will assume any others are probably important for some reason and not move them across drives during rename/move operations, nor compute their size during things like site size, etc.
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