Treenails are, shall we say, a bit of much discussion. On the real thing, the holes were drilled, the treenails set and then a plug of the same wood as the deck was put in to cover the treenail. For the most part, they're pretty darn invisible. BUT.. we modelers like to show them off.
You could use a very sharp #2 pencil for the impression of a treenail by doing it just before putting on the finish. The pin and colored filler seems popular. Or use the #80 drill and draw some treenails down to that size. Some also use a hyperdermic needle to leave the impression of the plug.
The final alternative is just to not do treenails since anything smaller than 1:64 is pretty darn small.