The first hit I get by googling "codesys raspberry" is: http://store.codesys.com/codesys-contro ... pi-sl.html
There is talk on that page of Raspbian, so yeah, it appears to be an application that runs on top of the normally expected operating system. It's still possible that the program does things that make it not portable to the latest versions of Raspbian, or to Pi3 hardware, but that's moderately unlikely. The actual "will it work on a Pi3" question can only be answered by CoDeSys, or someone who has already run it there. You could download it and try it before buying a license.