While the Vita Muramasa isn't a straight port, it is true that the Vita overall has not been a very successful platform. But I'm quite sure Sony doesn't get all the money from PSN sales -- though the money is probably split with the publisher, not the developer, and thus Vanillaware probably doesn't directly get any money from it. It depends on the exact nature of their agreement.
However, PSN sales do show that Vanillaware is a company worth supporting, making it easier for them to find companies willing to front revenue for development. It's all about expected return on investment. Atlus most likely picked up Dragon's Crown because it was a good fit for their niche market, and because Vanillaware is a proven developer. Digital sales of their titles will help show that they can succeed in that market.