Testing a hypothesis! Resist on Plaster Mold 

It’s clear from your experiment that plaster surrounding the clogged areas is pulling moisture from more than just the slip directly above where it contacts. It pulls the closest moisture which is at times where the waxed areas have slip. My thought would be to use wax discs slightly thicker than you wall thickness and melt apply them to the mold wall. That way, there’s no slip there to pull. And you can just melt that wax off on bisque. Problem is, the piece won’t pull with the wax melted to the mold wall, so you’ll need to put the whole mold (piece and all) into an oven the release the wax from the mold before you pull. You’ll probably know where the piece was from residue for putting on the next discs for the next casting.

I like the idea of the wax plug through the mold wall. I think that you could push in the plugs from the outside so they would protrude farther than your wall thickness, and come time to de-mold, you could just push the plugs all the way through to the inside. It would be interesting to see the result of such a method on the inside surface... I wonder if the hydrophobia of the wax plug would create the opposite result as you found with the nails (a sink rather than a mound) The plugs could be solid wax, waxed candle wick, or some wood dowel soaked in molten wax. I'm not sure silicone spray wouldn't also soak into the adjacent plaster affecting its performance. There might be a source for wax rods for use in jewelry investment casting.

Would dipping the nails in wax solve the size and surface tension issues? I work in beeswax mostly, but paraffin would coat the nails. Or perhaps a silicone spray on the nails would work also and be cleaner.

Heres my idea, hear me out: 3D model the nails and make a mold that contains enough for a plaster-mold's worth. have them all attached to a central block. Print the mold in ABS/PETG. Pour liquid beeswax into the 3D printed mold (wax should release). Pull out the beeswax cast and then you have wax replicas of the nails. Cut from the molded block and insert into your plaster mold. Cast. Success. My guess is it will reduce the buildup on the inside, but not resolve the search for perfect internal holes; if there is such a thing.