Thanks ethanay, I had exactly the same two problems as you!
Personnally I've put "hdparm -B 254 /dev/sda" even in battery mode because this 
"click" sound is driving me crazy. My HD temperature looks OK (42°C).

I'm not sure the problem is 100% solved thus, because I still hear a
much fainter "click" sound, which is happening every 1 second
approximately, and I also hear my disk spinning quite often without any
reason...

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High frequency of load/unload cycles on some hard disks may shorten lifetime
https://bugs.launchpad.net/bugs/59695
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