I think he wrote "emergency commands" not "hacking commands".
Because she's inside the same network, she can send those commands from her cubicle, so she needed to know how to do it.
Side note: Why is everyone using Kali Linux all the time? Does anyone (who isn't 14) really run that as a daily driver? They use it to surf the web and check their email. It makes no sense.
There's a scene where we can see Elliot running CentOS on his personal laptop. Not that lends any realism (CentOS is more common on servers, not PCs) but it does show their awareness of Linux beyond Kali.