Thanks for the good advice. That is what I'll do and I'll post result here.
Not having lived in NE in several years (18 in fact) was what got me in this spot in the first place. Most recently I had lived in CO (since 1997) and have just moved back a couple of years ago. The friend who was with me (also from CO) got the same ticket as we did exactly the same thing, remove the round from the chamber, pocket it, and stick the guns into cases behind the front seat of the truck. I am certain (now) that the law states that this is considered a loaded gun as I have since looked. And I refused to sign the ticket until the Conservation Officer wrote on the ticket "two shells in magazine only".
Maybe a good followup question should be "I know that I'm required to show my hunting license(s) to any game warden that asks, but am I required to show him/her my weapons as well? Or does this type of search require a warrant?"
What got us in trouble is that we thought that we had done everything by the book. Do we have other weapons other than the muzzeloaders in the front seat? Sure we have shotguns behind us in cases! You want to look at them? Sure, here we'll get them out so you can take a look!