Well, mystery is a big theme. Since Bendy comes from a rather spooky and unexplained world in the original concept, fanfictions often play on that. Also, the theme of trust. As the reader gets closer to Bendy, there's a development of trust between them. And there's also the theme of discovery, like the reader discovering new things about Bendy and his world.
One of the main themes is the contrast between the normal world the reader is from and Bendy's ink - soaked world. This contrast creates a lot of interesting situations. Another common theme is protection. Sometimes Bendy protects the reader from the dangers of his world, and other times it's the reader who protects Bendy in some way. And of course, there's the theme of connection, whether it's a spiritual or emotional bond that forms between them.