source:src/allmydata/__init__.py contains code that is intended to suppress this warning, but says to do so only when it comes from twisted:
# This warning is generated by twisted, but not when it is imported, only on an error.
warnings.filterwarnings("ignore", category=DeprecationWarning,
message="BaseException.message has been deprecated as of Python 2.6",
module=".*twisted.*", append=True)
I think this should just be changed to a global filter, i.e. delete 'module=".*twisted.*", '. This particular deprecation is not important and doesn't ever merit bothering any end-user.