I don't think such theories were a direct source of inspiration either, I was talking more about the themes in general. The paragraph on the thematic differences between Parasite Eve/SnU got me thinking a bit. As you say, the topic of social alienation could be influenced by a variety of sources, novels like No Longer Human and similar works. Still, the emphasis on sex and violence and the breaking of social taboos reminds me of Freudian themes a lot even without being directly influenced by them.
There are some interesting parallels between a few of the game's themes and Freudianism. The opposing points of view of Saya/Fuminori and Koji/Ryoko are the points of view of being engaged in society and being alienated from it. On Freud's theory, of course, the mind is not a harmonious whole, as conflict breaks out between humans as social animals following the norms of their community, and their various individual tendencies that don't perfectly match with said norms. And a similar conflict takes place in the narrative, where one side feels an imperative to terminate a threat to society, while the other feels necessary to do things their own way. And I think this creates a sense of ambivalence in the story, both sides are easy to identify with as both points of view are experienced by everyone to some degree.