Hi,
I'm experiencing the exact same issue on some of the cPanel accounts. After unsuspending an account it shows 404 error on the website and gets resolved automatically after 20-30 minutes. The accounts usually get suspended/unsuspended through WHMCS and cPanel API. Also tried this through WHM and experienced the same on those problematic accounts. Looked into the logs at /usr/local/cpanel/logs/error_log but there was no error. Also tried restarting httpd, dns, php-fpm immediately after unsuspending problematic account but restart on these services doesn't seem to resolve the 404 error on website. As mentioned earlier the 404 error is gone within 30 minutes of unsuspension.
My clients get panicked when they see 404 error on their websites as WHMCS is set to automatically unsuspend the hosting account after payment through module action.
Did you find any resolution for the issue? It looks like something needs to be restarted/checked after account unsuspension and it take place after 20-30 minutes.