Was wondering about this as well.
+1
As an author, I have thought about this myself. I came up with two reasons, maybe there are more.
The author of TNT (Torah Novel Thoughts) is a friend of a relative. He wrote something he thought was controversial and decided he wasn't interested in the
potential negative feedback changing to personal, and the only way to contact him is (as I can recall) an email address. He certainly has an intense writing style, but I don't recall reading anything controversial.
https://www.amazon.com/TNT-Torah-Novel-Thoughts/dp/B00Q3HBHCYHumility is another reason, especially when books are written by talmidim. However, I personally wouldn't take my name off a book myself because of this. Writing anonymously is commonly used when a person is not willing to face up to what he says, and this is one of the dangers of the internet where almost everyone goes without a true name. The stigma attached to that means that anyone who wants to accomplish something in the world needs to stand behind what he writes or risk wasting his work. On the other hand, novels may not be written to accomplish this (sometimes), but rather, an idealogue just wants people reading his book instead of anything else so can afford anonymity. (IMHO a voracious reader cannot be satisfied by Jewish literature if he/she does not get the same satisfaction from seforim, because there just aren't enough books and they also cost too much. In my teens, I read six or more books a week.)
Agav, as a few users know, my name is not on the one sefer I did write, because I was paid to ghostwrite it. Ironic, perhaps, but the sefer I am working on
now will IY"H have my name.
EDIT: I suppose a third reason is disassociation, if the real name would result in more people not taking the book seriously.