It it still true that generating bindings for luajit is easier than with plain Lua? When I used it for a toy project that was the main reason I chose luajit, especially since the project was written in c++.
Writing bindings isn't something I have a lot of experience with. The main difference I'm aware of is the FFI system, which creates bindings from C headers, and will result in faster calls with good JIT support. I assume it introduces some extra security challenges if you care about that. You'll still probably need to write some wrappers, either C-side or Lua-side if you want a nice API. I know there are other tools for creating bindings, but again, not my area of expertise.
In my experience it very much is. Most of the LuaJIT code I write is just metatable classes around C libraries like SDL. Just being able to write C structs and lua functions is a dream. Having to manually deal with the stack from C-side is a PITA.