Simplify3D is actually already a full 64-bit application. The reason you are seeing that warning is that we use a 32-bit installer which allows us to provide compatibility for older systems. You shouldn't see the warning again when using the software, it only shows when you run the installer.
For reference, you can also verify that Simplify3D is a full 64-bit application on your own by following these instructions. Open the System Information application on your Mac, go to Software > Applications, and then click on Simplify3D in the list to the right. It will say:
64-Bit (Intel): Yes