The rims were made for road racing. Rim brakes will work just fine. The nipples should be about 3/4" long. If yours are too short, get the right ones. Personally, I would not use aluminum nipples. And there is no need to ruin the nipple screwdriver slots by grinding them down. The sew-ups will glue (or tape) up just fine right over them despite the nipple head "protruding", so don't worry about it, and don't ruin the nipples.
Amazing how much BS lore about the past is so readily believed.
This 36-spoke Scheeren Weltmeister front wheel is lighter than my carbon front wheel, with tires mounted.
If that Hi-E frame is not in the esoteric components thread, it should be!