Why did they hammer nails in half way and bent them over to secure supports?
The nail heads aren't big enough for the holes. At that time carpenters didn't enjoy the vast array of fasteners and installation tools that we do today, so they may have used what was available at the moment. It did the job, right? 

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The carpenter had intended to replace them with lag screws and forgot.

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There's something sensitive to puncture behind the surface of that lumber. It looks like a standard beam, but it's hard to say from my house.