If pregenerated janex index is found, it is used.
But unless you have extremely big jars and lots of classes this shouldn't change boot time in any big way.
I would look in different parts of your deployments, like jpa / hibernate schema validation / updating which really slows down the boot.
Best to profile with some java profiler like yourkit or jprofiler to see what parts of code take most time.
Once you have that, we can help you understanding what those results mean in context of what to do with your deployments.