I worried a lot about dress for dinner prior to our cruise - and never once thought about it on the ship! Our sons are teens, and followed the dress code, however no one in the dining areas seemed to pay any serious attention to the clothing on those around them - I know I didn't. (And really - once they are seated, who knows whether they are wearing shorts or long pants! ) I was much more concerned with relaxing at the table, enjoying my dinner and conversing with DH and DSs. I truly think that as long as people are clean and neat, that is what counts - with the exception of formal night. (And on formal night, you have the option to eat elsewhere if you choose not to get formally dressed up.) There are many debates on this board concerning dress in the dining rooms, and I know that is one reason I stressed out about it. It just doesn't seem to be that much of an issue on the ship!
I used to dress my sons, when they were younger, as you describe dressing yours - they were only 22 mos apart in age and looked adorable in matching outfits. I would have dressed them in shorts if that is what they were most comfortable in at the age, had we cruised back then with them. JMHO, but then again I think that my work as a pediatric nurse practitioner to a very indigent population has reinforced what my mother had always taught me - never to judge people by any other way except how they treat other people and animals!
Enjoy your trip - you can't believe how wonderful it will be and how many lasting memiories it will create.