Based on my first impression, these tools are very confusing. They both seem to create a connection file and only the Create ArcSDE Connection File tool allows you to connect to an ArcSDE Application Server. I could study the differences in detail, but that might mean that the tools are not intuitive or clearly labeled. Since the end result is a connection file, it would be better to just have a Create Database Connection tool that lets you connect to an ArcSDE service. In the future, you could deprecate when you like.
