Oh my god, it's so stupid. It turned out that my issue was hddtemp
running in daemon mode. Because it uses smart (sic!) to query drive
temperature, and update interval is hard-coded to 60 seconds, it was
waking my drive every 60 seconds! As soon as I disabled it, my problems
seem to go away. The drive spinned down and doesn't wake up for several
minutes already, just like it should. =^_^=

So for the rest of you, check that you don't have anything checking
smart in the background, hddtemp in particular...

P.S. On the side note I find it crazy that to check drive temperature
you need to spinup... x_x ...I couldn't even suspect that!

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