You're absolutely right, I just honestly don't think Nintendo put any thought into it being like this so I don't think it applies. I could be wrong though. The spelling is different for the Boko creatures (Boko Baba/Bokoblin), but I figure that's only so it looks similar to "Deku Baba/Moblin"...
BOH-KOH-BLIHN, like cocoa.
While that was my first assumption on how to pronounce it, it also always made the most sense to me, considering what the term "boko" actually was in the game the term first appeared in (The Wind Waker), which was merely an enemy name prefix. We forget this now...