The Louisa showing in 1939 might be his second wife, because there is this possible marriage:
Marriages March quarter  1939   
 John Cunningham   Leeds North    
 Louisa Lowther    Leeds North   
There is also the possibility that Louisa might have been married before, so the blacked out entry could be a child of a first marriage for her, or a totally unrelated person.
Mary is shown as Cunningham/Flanagan, and I have previously posted a possible marriage.
This is followed by a death
Deaths June quarter 1960  
Mary C Flanagan age 25 in Leeds   2c   144   
Cannot see any births for children of the marriage.
There is this possible first marriage for John:
Marriages June quarter 1933  
John W Cunningham    Leeds North    
Clara Howden     Leeds North   
but cannot see a death for Clara (nor a Leeds birth for Clara Howden)
It depends how much you want to spend to try and check if these are the correct records.