FAA guidance on the number of threads required
When installing a bolt and nut, the typical rule of thumb is...you can use up to three washers and you should have one to three threads showing....but you must also consider the length of the bolt, since grip plays an important part in the equation. 43.13-1b gives us guidance on this, since the grip should extend the entire length of the hole(in a perfect world). In the following exerpt from that document, you are limited to using 1/8" of washers, not necessarily three. The typical length of threads on an AN bolt allows this much and still allows a thread to show on the nut after installation. If you can't get at least one thread, either you have more than 1/8" washers installed or the bolt is too short.
Per 43.13-1b Chapter 7-37.
GRIP LENGTH. The maximum combined height of
washers that should be used is 1/8 inch. This
limits the use of washers necessary to compensate
for grip, up to the next standard grip size.
AND
All bolt installations
which involve self-locking or plain nuts should
have at least one thread of the bolt protruding
through the nut.
The above applies only to AN bolts. Other hardware, such as an 8-32 threaded machine screw, technically does not have a limit to the number of threads that can show, although using the same rule as for bolts is a good practice.
Good luck.