How much time on average does it take to the website to be updated when you modify files or settings (more like a quarter or 3 hours ) ?
In normal cases instant. Please clear your browser cache and try again.
If your domain is linked with CloudFlare, then CF cache expires in 4 hours unless you login to CF and purge it.
Is there a command to instantly apply modifications (with no attention to people possibly on the site)
and by the way, is it gonna wait for people to disconnect or will it kick them out ?
What do you mean? All settings from 000webhost cPanel (except the ones from email forwarder/domain sections) are propagating instantly. Also, there is no need to kick out clients to apply changes to your site from File Manager/cPanel/phpMyAdmin.