I'd not recommended Spring Data REST approach for production level APIs as you wouldn't have much control on the REST resources you expose. Suppose in near future, you'd want to embed some data in each document of the result array before sending it as response then you'll end up following the second approach.
So, in a nutshell: Use Spring Data REST for quick prototypes where you want to CRUD of models whereas in production level APIs following separate Repository + Service + Rest Controller so that there will be consistent and clean code.