There is a 60+ page thread in here that is all about the 30 second beachball hangs.
That issue is completely different than the click/beep problem and affects a wide variety of drives, even stock drives from Apple.
The cause of the problem, in a nutshell, is that the EFI version 1.7 firmware is broken. And I suspect that many who have been focused on the click/beep problem will find they are affected by this firmware issue as well.
The only workaround at this point is to go into an Apple Store and have your firmware downgraded to version 1.6 (which will also limit your SATA interface to 1.5Gb/s). On the plus side, this downgrade only takes a few minutes, and is completely reversible if you change your mind (just install the firmware update again through Software Update).
Apple has not officially acknowledged this problem, much less said anything about fixing the broken firmware.
I put up a video of what this firmware issue looks like here:
http://vimeo.com/5854152
If that looks like what you're seeing, make a genius bar appointment and ask them to downgrade your firmware. Also, write Apple some feedback (
http://www.apple.com/feedback/macbookpro.html) and ask them to fix this issue.
Note that this issue ONLY affects mid-2009 13" and 15" MacBook Pros (the ones with the new SD card slot).