Thanks, they have been removed. I also have a tool that detects duplicates, just hadn't run it on LWJGL 3 before.
It's normal that you've found so many duplicates, but most of the duplicate constants in extensions cannot be removed. It's only OK to remove those that have been defined in a core version less than or equal to the minimum version an extension requires (e.g. ARB_shader_subroutine requires GL 3.2 so UNIFORM_SIZE and UNIFORM_NAME_LENGTH, defined in GL 3.1, could safely be removed). I did this manually in LWJGL 2 (might have missed some, let me know if you find any), but I plan to "annotate" extensions in LWJGL 3 with the minimum core spec required, so that future cleanup can be done automatically.