In NC, the DMV uses the same tag renewal form for everyone (I suspect most states do this as it saves a lot of money...) so you get a blank for the DOT number even on those registrations that don't need one. Every one has instructions on the back forwalk in, mail in, and online renewal (and a little line at the very bottom of the form that states that you can't use on-line renewal if it weighs over 10k lbs...). When you get a tag renewal sticker and the updated registration card you spot a note about IFTA stickers on the card even if you are registering a two axle vehicle (since the note is based on weight on the assumption that most heavy vehicles have three or more axles...).
So, I'd go with the N/A in the blank. It lets them know that you didn't forget to fill out the form completely and alerts them that you are exempt from having the number. It should go right through (especially since it has been done before without one and the file should pop right up when it is keyed in...), but if not, just explain politely to the person at the DMV office why you don't need one. If you go in with an attitude, and piss off the clerk, you'll just tick them off and they'll look for ways to make life difficult...