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In Excel 2011 for Mac, you could either use a system call or MacScript("do shell script ""command"""), see http://stackoverflow.com/a/12320294/918626.
In Excel 2016 for Mac, I can still do: MacScript ("do shell script ""open /Applications/Calculator.app"" ") but already something like MacScript ("do shell script ""source ~/.bash_profile;open /Applications/Calculator.app"" ") fails (which worked on 2011).
I saw http://stackoverflow.com/a/30949324/918626 regarding MacScript in general, but I wonder if it is also the easiest way to call a shell command?
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Yeah, I made the same experience... system and MacScript seem to both work for very simple things. AppleScriptTask was about the same experience... unfortunately....
As Ramit explains Office 2016 runs in a sandbox which means it only gets access to predefined resources.
Checking the sandboxd messages in Console can help to determine why an operation failed. I suspect there isn't ONE best way to call a shell command as it depends on what the scripts does.
UPDATE: Within the limits of the sandbox a system() call still seems to work. Leaving the sandbox is possible using AppleScriptTask in theory. However, I couldn't get it to work reliably with anything but the most basic script.