Anime has a very small fanbase and small distribution. A good anime with good animation, good soundtracks, good plot, good dialogue with good actors is going to cost a lot. Not to mention the licensing and localization.
Anime in the western region produces large quantities of the more popular animes so it's going to cost less but that still doesn't make up for the small audience, a good portion of which such as @The Hero of Time who torrent or even worse stream the show not only not supporting the studios who created the show but the streaming network for simply having it in public display in lesser quality.
A good way that large companies counteract the cost of all this is by making less copies & simply charging a lot to those who they know are going to buy. The collecters. The ship merchanters and the insperationalists. To keep them more rare and collectible is why they make less copies.