Say I have two Maven dependencies defined in a project like below.
com.thoughtworks.xstream
This feels really odd to me, and if it's "feature", I think it is a really dangerous one. Anyway, it's not a Maven bug and it's in the maven documentation here.
Regarding best practices on this issue, I haven't heard of any, but the safest way to proceed ought to be to entirely remove xstream from your pom, relying on the transitive dependency. Doing this will result in a build failure if the dependency to mylibrary is removed. This will act as a notification to you that you need to fix something. You won't silently loose required dependencies, and you won't silently have dependencies you no longer need.
On a side note, mvn dependency:analyze can be used to check for dependencies that are included but not used.