The following steps are what I used to disable this warning on top of my VSphere Client to manage my ESXi 5.x servers.
- Select the ESXi 5.x host server in your Inventory
- Select Configuration
- Select Advanced Settings on the left under the Software menu
- Once selected find your way to the bottom where UserVars is located.
- Change the value of UserVars.SuppressShellWarning from 0 to 1
- Click OK
Another way to resolve this is to use the esxcli command via the local console or over ssh.
Connect to the ESXi host using the root credentials and run the following command:
esxcli system settings advanced set -o /UserVars/SuppressShellWarning -i 1
For the source of this info and additional steps please check out the VMware KB 2003637