I have no experience with the CIS benchmarks, but I expect that it enabled a security group such that port 3838 is no longer accessible.
When you connect to your EC2 instance using ssh, is shiny-server still running? Can you connect to http://localhost:3838 using curl?
If the answers are "yes" you should change the security group applied to the EC2 instance to allow incoming traffic on port 3838. Or configure Shiny server to listen on another port which is accessible from the outside.