There's the thread runout region that needs to be avoided, so the nut doesn't bottom out, and the full shank, I believe, has to extend 1/8" past the shear plane for the threads to be excluded, so that combined with the 1/4" length increment, is why the minimum 1/2" plate thickness is in the AASHTO spec. If you need the extra shear strength for a connection with a thinner plate, you can do the math and see if the standard dimensions work, or specify a specialty bolt with a specific thread length.
For bridge design, I can't see it becoming an issue, anyway, since the capacity of connections with plates thinner than 1/2" is typically controlled by the bearing capacity of the metal around the hole in the plate, and not by the shear capacity of the bolt, with the possible exception of a connection with filler plates of substantial thickness. However, we only use filler plates on girder flange splices, where we almost never use splice plates less than 1/2".
So basically, in steel bridge girder design, we exclude the threads from the flange splice connections, but include them for web splices and most other connections.
Rod Smith, P.E., The artist formerly known as HotRod10