I ordered a battery hold down from Ames for my 57 Star Chief.  It came with 4 holes drilled into the sides of it.  These were not factory holes.  I called them with my concern and was told they drill all of them in house!  When I asked why, he could not explain the reason.  Anyone have an input to this??  The hold down fits tight against the side of the battery, so you couldn't get anything into the holes even if you wanted too.  I'm attaching a couple photos.

Apologies for not seeing your post earlier.

Those are essentially drain holes. Back in the day, before sealed batteries, 6V and 12V batteries had individual cells and sometimes the car owner would have to top off a cell in the battery with some water. Sometimes these unsealed batteries would leak battery acid and it had to go somewhere (away from the top of the battery) or water from rain or snow would get into the battery tray. In either situation, you want to drain the liquid away from the battery so as to not damage or short it.

There doesn't appear to be access holes to top off each cell, (sealed) but would go with the drainage idea as there appears to be a track running behind the holes.  What jumps out at me is that you might have installed the hold down backwards?  There is a half moon cutout on the right side,  if flipped around, looks like it would be a cutout for the post on the other side.  Also looks like its a shorter side to give you more space on the other post. (going off the distance from wingnut to inside edge)  Might let you make full contact top to bottom, on the post.  Looks like you have it mounted up high on the post for clearance (so it's not touching the hold down?)

Justag, thanks for the reply.  The battery hold down is actually made for a battery with opposing posts, which of course this one is not.  So flipping it wouldn't make a difference.  As for it not sitting down on the battery, it's because this battery has a ledge on both ends and won't allow it to go all the way down to the battery.  When it's time for a new battery, will get one to fit the hold down, but for now......... 

Still don't know how those holes on the side could be for drainage.  If the liquid got to those holes, it would just run down the battery into the tray, whether the holes were there or not.