Java is statically typed. Clojure is not. To me, this is the biggest difference and the reason to choose Java.
This was mentioned briefly here: https://hortonworks.com/blog/microbenchmarking-storm-1-0-per...
The Clojure based core has served the community well for some time. It was still powered by Disruptor (a fast Java messaging library). So there was always some back and forth between Java and Clojure.
For Storm 2.0, the Java rewrite happened first. The re-architecture work might have not happened without it (at least for the foreseeable near future)... primarily due to Java expertise being more easily available.