There are three distinct layers to Storm's codebase.
First: Storm was designed from the very beginning to be compatible with multiple languages. Nimbus is a Thrift service and topologies are defined as Thrift structures. The usage of Thrift allows Storm to be used from any language.
Second: all of Storm's interfaces are specified as Java interfaces. So even though there's a lot of Clojure in Storm's implementation, all usage must go through the Java API. This means that every feature of Storm is always available via Java.
Third: Storm's implementation is largely in Clojure. Line-wise, Storm is about half Java code, half Clojure code. But Clojure is much more expressive, so in reality, the great majority of the implementation logic is in Clojure.