I have done some testing on a cPanel server with 11.50.0.10 and CSR generation is still using SHA-1. Any certs that are good until 2017 will have to be reissued soon as Google Chrome will complain. If you are looking to generate a CSR with SHA-2, you will have to do it via command line. You can use something like the following below.
openssl req -new -newkey rsa:2048 -nodes -sha256 -keyout mydomain.key -out mydomain.csr
