They are just dummy files.   Don't delete them, but dummy them.

Companies put pad files in umd games, because it will push the data farther to the edge of the umd disc, so the game will load faster.  (The PSP reads the UMD disc from outside to in.)  So obviously these files are completely useless to someone loading the game from memory stick.

Also, you can safley dummy the contents of the sysdir/UPDATE folder    ;)