It sounds more like a family thing. There is definitely NOT anything in LDS doctrine that says little boys must always wear a shirt. Heck (see know you know I'm a Mormon
) My brothers went shirtless all the time in the summers. Modesty is a big concern and is emphasized in our church but never anything like ALWAYS wearing a shirt for a little boy... it seems a bit strange that the former FM was QUITE upset about that.
The only other thing you might run into is that Mormons don't drink cofee, tea or alcohol and they dont use tobacco of any form. So there may be some questions and some issues there if the kids have been told that those things are a no no. So depending on how ingrained those things are you may need to explain that different families make different choices about those things and that neither way is "bad" or "wrong" just different choices for different families.
Other than that I cannot forsee too much of an issue. They are in your home and your beliefs, morals, and rules should be respected. If you have any other questions please feel free to ask.
~Rachel