Applying SET (M) for my wife however children are born here

Hi

I am going to apply for my wife's ILR next week. My children are born here and have been granted two years FLR recently. I believe that my children can apply for British Nationality at any time as they were born here however as we are planning to visit to my home country and we can't keep dual nationality, I don't want to apply for their nationality at this stage as we will have to go through the visa process. My question is If I don't include them as a dependent on SET (M) and take them to my home country for visit, will I be questioned while coming back to the UK as they will be on FLR & we will be on ILR. I understand that there shouldn't be any problem however just anxious to get it confirmed.

Thank you for your response in advance