Nail knots can fail on monofilament core flylines. That is, the knot can cut thru the outer coating of the flyline and slide off the core. Monofilament cores are pretty standard on both intermediate and sinktip flylines. Floaters are typically multifilament core with a large radius of outer coating. Nail knots, or even better, needle nail knots, are fine on floating lines.
If you are still inclined to use a nail knot, I would suggest you use a double nail knot and coat it with Aquaseal or Knot Sense.
Since I use Rio flylines, the factory loops have proved to be robust and loop-to-loop connections with a cat's paw provide a pretty slim connection. Flylines without a factory loop can be upgraded to loops with braided double-catch loops that are 100 per cent. Loop knots for the butt section can include the perfection loop, double surgeon, or the Kreh loop.
In on-the-water emergency situations, a must know knot has got to be the nail knot. While Juro uses a double eye needle, I have found that a two-inch long tube from a WD-40 can works well for me.
There is a host of approaches for connecting leaders to flylines, but I want the strongest connections I can get, and that is what prompts me to use the outlined methods.