So... is Mangaka-san to Assistant-san to The Animation finished or not?
NO, it is not finished.
Why?
The anime finished after the manga:
Anime finished: June 24, 2014
Manga finished: June 06, 2014
... But MangaUpdates contains information about the anime adaptation and indicates that it is incomplete.
Watching Order (by release date)
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Synopsis
Mangaka-san to Assistant-san to The Animation follows the daily life of Yuuki Aito, a manga artist with a rather peculiar obsession: panties.
He is constantly surrounded by his female assistants, who become the frequent targets of his, shall we say, "artistic" requests.
The series explores the comedic and sometimes awkward situations that arise from Aito's perverted tendencies, contrasting them with glimpses of his surprisingly kind and helpful nature.
The assistants find themselves grappling with their feelings towards Aito, torn between his admirable qualities and his often inappropriate behavior.