The root section has a folder named scripts for WHM/Cpanel and other aspects of maintaining your server for your website right? Trying this ssh command,user@domain[~] cd /scripts, it told no such file or directory.

How can I re install/recover this script directory? Should I contact our web host provider? Or I can recover/re-install/create it easily by myself?

I am using CENTOS 6.6 x86_64 standard. I tried to restart apache from WHM and it hangs. Now my website and whm are not showing. Maybe it hangs because the script for restarting apache was already deleted.

Did you do that entirely as one command?
I'm not sure that's a valid ssh command
Perhaps try just logging and and then cding?

I am using putty.

I can use that cd/scripts and it says NO such file or directory. A server provided by a web hosting company should have a directory scripts under the root right? Our other server has this script folder. I think I have accidentally deleted this script folder.

This folder scripts contain scripts like /scripts/easyapache, /scripts/updateuserdomains, /scripts/ftpupdate,/scripts/rebuilddnsconfig

How can I recover/re-install it?

If the directory / files have been deleted, and you are using this from a hosting provider, the correct action would be to contact them.

Look to see if there is a directory for /usr/local/cpanel/scripts/ Not all, but the major scripts will be duplicated there. In the mean time you would want to have the issue addressed to cpanel. They might need a case connect but you can ask about this in their forums as well.

https://forums.cpanel.net/
cPanel Forums