Graphql gives a better way to request nested schemas and handle relationships and recursion. But when you cross that line, the client now would get ideas and starts asking "Why not be able to do that operation on the 5 level deep object?". Now you have to either not allow the client to do that, or you have to "rewrite the database" to make recursion optimal.
This is not a problem of Graphql. This is an HTTP problem. When you need to promote the database querying layer over HTTP, then you have a problem regardless.