Your child was granted a UK Standard Visit visa, with the proviso that he be accompanied as he is a minor (under 18), in this case by his mother. She agreed to this condition when the visa was issued (and the visa does allow for both parents to be named; why were you not included?).
The UK does have exit checks on all passengers leaving the country, through passenger records and predominately used for immigration and data purposes. Your departures (for you, your son, and your wife) will be reflected in your immigration records, and it will show that the child entered with his mother, and left with someone else.
As your plans constitute a material change to your son’s visa, it may be best to Report a change of circumstances if you have a visa or BRP.
And should you leave with your child and not encounter any issues doing so, depending on circumstances, it could affect future visa applications, for both you and your wife. It could be viewed as a serious breach of visa conditions, which the UK does not look upon very kindly.