The different filesystems sounding different phenomenon would probably be due to different cluster sizes. A freshly formatted hard drive will be full of all the same value. Any file written to it will only fill up the start of the cluster, leaving the end the same - thus making no sound.

Data     :ADRGESHTFDZDRSRGSEWERT00000000000000000000
Waveform :/\/\/\\\\///\/\/\/\/\_____________________
Lots of files together will make a more regular wave:
Data     :FF00F000FF00FFF0FF00FFF0F000FF00
Waveform :MM__M___MM__MWM_MM__MWM_M___MM__
If the cluster size is smaller, the clusters will be closer together, and the frequency of the envelope higher. So NTFS would sound higher than a normal fat32, which would sound higher than fat16. (I suspect my 300 meg, ridiculously small (256 byte, IIRC) cluster fat32 partition would screech!)

The blank space at the end of the cluster would only get overwritten if the file were deleted (or moved by a defragger), and a file larger than one cluster were written to it. It's not inconcievable that this slack space could stay blank for many years. Older filesystems might sound different... unless said defraggger overwrites the free space.

(conjecture: If the drive is formatted with a regular pattern instead of just the same byte over and over, it would beep instead of being silent... I don't know enough about unix filesystems to know for sure.)