An easy problem.
It seems like nonzero fixer can only fix definition, not usage. nonzero fixer cannot fix problems like below:
 a = 1
 a.__nonzero__()
And there are no cases of __nonzero__() usage in test cases from test_fixers.py.(all cases test only definition rename)
It might not be a bug, since in DOC it just says "rename", not "convert". (If it is not a bug, the doc must be considered to be kinds of confusing and should add additional description.)but adding this automatic transformation is really useful in my current work, so at least an optional fixer is needed for 2to3.
A fixer of __oct__(),__hex__() to oct(),hex() is also in need, but 2to3 lacks such fixer.

I suspect these fixers were left out simply because no one expected anyone to call the dunder names directly; the whole point of the dunder names is that they're not used directly, being invoked by syntax/context (__nonzero__ being the first thing tried for implicit boolean testing or calls to bool/operator.truth) or by top-level functions (__oct__/__hex__ being called by oct/hex).

The only legitimate use case I can think of off-hand would be in class hierarchies, where a child dunder method is implemented in terms of a super() call to invoke the parent.

Do you have any examples of code bases that rely on this? I've never seen one personally, but I'm not about to claim exhaustive knowledge of all Python code in the world.

Got it.
I am just testing all changes in Python 3.X (in preparation for a project porting to 3.7 before I have permission to view the source code), and call __nonzero__() directly for testing. So maybe I cannot provide an example. 
I did not realize that it should not be called directly.
Still, I recommend a documentation change to explain this fact, telling readers the fixer will not change the usage of __nonzero__().
Thanks for your reply.

If no one going to provide documentation changes I propose to close this issue.

New changeset 481f3ffdbe40bd19677a1ba0ac2e7cece8949b47 by Irit Katriel in branch 'main':
bpo-37602: Clarify that the lib2to3 nonzero fixer changes only definitions (GH-30075)
https://github.com/python/cpython/commit/481f3ffdbe40bd19677a1ba0ac2e7cece8949b47

New changeset 80eb8ab81fbe46497f16071b311c9d8e13ec2d3b by Miss Islington (bot) in branch '3.9':
bpo-37602: Clarify that the lib2to3 nonzero fixer changes only definitions (GH-30075) (GH-30083)
https://github.com/python/cpython/commit/80eb8ab81fbe46497f16071b311c9d8e13ec2d3b

New changeset 310bae628a9b065d29dbdbf4f7f5beb9fcc72ace by Irit Katriel in branch '3.10':
[3.10] bpo-37602: Clarify that the lib2to3 nonzero fixer changes only definitions (GH-30075) (GH-30085)
https://github.com/python/cpython/commit/310bae628a9b065d29dbdbf4f7f5beb9fcc72ace