If all of her documentation uses her maiden (pre-marriage) name then I believe that this is the correct answer. You should answer truthfully but, from what you say, she has. If you are also truthful then I cannot see how this would prejudice your application. Of course, if you need to prove that you are married then your names will not help and you would need your marriage certificate but I expect that you would anyway.
The tradition here in the UK is that a woman takes her husband's name on marriage but it is increasingly common for women to not do so. I don't have any statistics but in the sample of my family (me, one brother, and two sisters), I am the only one who shares a surname with their spouse. Many of my married, female friends and colleagues do not use their husbands' names. It is also becoming common to use a hyphenated name and sometimes the man does as well. I don't expect that anyone (outside of remote areas) would be surprised by a married couple who did not share a name. Someone working with visa applications must be very much used to this. The only rule today on what name to expect someone's wife to use is to not expect anything.
Suppose Alice Smith marries Bill Jones. Traditionally, she would change her name to Alice Jones. However, today, she might remain as Alice Smith or change to Alice Smith Jones, Alice Smith-Jones, Alice Jones-Smith, or maybe something else. The man might change as well e.g. Bill Jones-Smith.
And this just covers straight marriages. Of course, there is no long standing tradition for other cases so each couple makes their own decision.
