It appears if I use PEP-526 for class-level variables I must document them in the class's docstring in which case I need to pick my favorite way to do this.
Python 3.6.4 pylint==1.8.4
class Joe(object):
counter: int = 0
"""This is a counter"""
pylint says (correctly, regardless of whether the variable is assigned to):
W: 3, 2: String statement has no effect (pointless-string-statement)
It's not PEP 526 being incompatible with the docstring; it's Pylint not understanding what you've done. Wait for an update.
Some tools support a concept of docstrings for class variables, but it's never been part of Python itself, and PEP 526 doesn't change things.