Whilst I understand the process of adding both maiden and married names to the register...I have one entry where the lady in question remarried in 1944 after losing her first husband in the second world war...however, her two sons have the surname of their Father who was still alive in 1939 but their Mother's married name is crossed out and replaced by her second husband's name...this could be misconstrued as it appears as though it is her maiden name and that she isn't married to the Father of the children.
I too have many absentees...but I can be patient as it is a great resource to have at your fingertips 
Carol
The inference would only be made if the person making such assumption does not understand the reason for the 1939 National Register and the reasons why and how it was updated.
For the period between 29 September 1939 and 22 May 1952 the 1939 National Register was a register for ID Cards and also at first ration books.
After 1952 it became a register for the workings of the National Health service alone (no ration cards, no ID cards) and therefore it was not so important to record names accurately.
During the war period it was very important to record people accurately, if a woman changed her name on marriage her ID card and Ration book would have to be updated, if her children did not adopt their stepfather's name (as many didn't) it was important that their names were recorded accurately as well.
The register was never about making moral judgements whether children were legitimate or not but simply a means to accurately identify and supply rations to the population.
Cheers
Guy