Did you regenerate your migration script after adding the hooks?
I would start by putting some print statements in the include_name hook to see how it is being called. You should see it called for every object in the database. You can then decide which names to return True for, and which ones to return False for. The example in the docs is probably a reasonable default:
def include_name(name, type_, parent_names):
print("Checking %s %s" % (type_, name))
if type_ == "table":
result = name in target_metadata.tables
else:
result = True
print("Returning %s" % result)
return result
Use that hook in your env.py and regenerate your migration script. You should see output for each object in the database.
Simon