(Actually, it does but that doesn't work.)
If you want remove a label or description, you can run
item.labels['en'] = '' item.descriptions['en'] = '' item.editEntity()
or
item.labels.pop('en') item.descriptions.pop('en') item.editEntity()
or
data = {'labels': {'en': ''}, 'descriptions': {'en': ''}} item.editEntity(data)
However, if you want to remove an alias / aliases, you must provide data with accordance to change-op-serializations.wiki (which isn't really convenient):
data = {'aliases': [{'language': lang, 'value': alias, 'remove': ''} for alias in aliases]} item.editEntity(data)
If you manipulate with attributes (like in the first two examples), you will get API error modification-failed: Must be at least one character long because Pywikibot fills the changed fields with empty strings (since they are rejected, this is wrong behavior).