I saved the honor to unlock Nuclear Missles for my Cruisers but they don’t appear as a valid option? Am I missing something? I’ve only owned the game since yesterday but I hope it’s not too obvious 
The nuclear missiles are only avaiable to the Order cruisers. That would be the reason why you aren’t seeing them 
Many thanks! My roommate (we bought the game together) thought as much but I couldn’t find a reference to it anywhere 