Whmcs is not vulnerable yet. There are thousands to tricks to hack something.
1) Kernel not updated --- rooting is possible
2) Improper or unsecured server ---- navigating to other user account on shared panel is possible
3) using whmcs third part plugins ----- Everything is possible...
If i was that hacker i would have planted a shell to maintain access to your host and do what ever i like to...
Perform a virus scan and malware to find out whats fishy on your host