Do the PHP exec, passthru and shell_exec functions really need to be enable?
Installation and Configuration
exec() is used to get file meta data, so if its not working audio and video modules could loose data from the original files if any processing is done to them.
jrPayment module uses passthru() if your wanting to use stripe as a payment processor this needs to be active.
Only place im seeing shell_exec() is in the CodeMirror plugin so that's probably ok not to have on if you dont use past code into editors or bb code blocks in your site.