It certainly is beneficial to intern at a job you'd like to get after graduation. There's no harm in that because at least you'd be building a network and gaining experience.
It's also not the end of the world to intern in a different semi-related field before going for the job you want. I know pastors/priests that have studied law, foreign languages, etc. and they still ended up in their current roles. The possibilities are truly endless and you're never limited to what you choose. Whatever you choose is a stepping stone, not quicksand.
On a practical level, interning will allow you to see the fairly mundane parts of being a youth pastor that you wouldn't normally think about, organizing rides, arranging for food, getting volunteer forms filled out, etc.
Not sure there is a correct answer to your question. It does not hurt to intern in a job you would like post grad. That being said, it certainly does not hurt to try something different. If being a pastor is the ultimate goal an experience in another field may help you relate to other people in the future.