Let's consider the options.
If a child is orphaned by the death of both their parents, it is usually a device which frees up the child to have an adventure--the sort which could never have been enjoyed if constrained by the banalities of family life. There may be some shuffling about among disgruntled relatives, but for the most part orphaned children in books tend to reach the end of their adventures having either created or joined the best family for themselves. While their struggles as orphans are evident, their triumphs are just as prevalent. As examples I present Anne Shirley, Harry Potter, and the Baudelaire siblings.
Now let's look at motherless children. There is no sense of adventure for these unhappy souls. They are usually stuck working through their grief while also trying to contend with the ill-equipped parent who is still around. Books in which the mother has died seem to require an awful lot of growth on the part of their young protagonists. In fact, that usually seems to be the point of the book--showing the reader how the child grows, managing to survive the dark pit into which they have been figuratively thrown. Surviving a dead mother is an adventure of sorts, but not a particularly fun one. Katherine Marsh's The Night Tourist, K.L. Going's The Garden of Eve, and Sally Nicholls' Season of Secrets all feature children who have recently lost their mother and are trying to somehow reach or retrieve their deceased parent. A notable exception would be a character like Phyllis Reynolds Naylor's Alice, who is several years removed from the death of her mother by the start of the series. Even though she still misses her mother--particularly the impact of her feminine influence in her life--her grieving and subsequent transformation has happened off-screen.So where does this leave us? I would say it's better to be rid of both parents and just get on with facing the world. Being motherless is simply too angsty. Do you have any examples to present for either argument?
