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I don't believe there's any way that you can prevent the Mac from mounting all "mountable volumes" at bootup. This is a consequence of putting two drives into a Macbook Pro...

Having said that, if you don't want the second drive drawing battery power, your best option is to just drag the drive's icon to the trash after the bootup process is complete. This will DIS-mount it from the desktop.

The downside is that to RE-mount it, you will have to open Disk Utility to do so.
 
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