Though I generally would not recommend disabling this issue as it exposes security vulnerabilities and all esxi commands should be issued through supported VMware APIs there are a couple ways to disable shell alerts.
get-vmhost | Set-VMHostAdvancedConfiguration UserVars.SuppressShellWarning 1
vim-cmd hostsvc/advopt/update UserVars.SuppressShellWarning long 1
All changes can be reverted by changing the '1' at the end of the line to a '0' to enable them again.
This is further explained in the following KBs: