When WordPress Does Not Provide an .htaccess File for New Multisite Sites because of CPanel Fantastico Auto-Installer?

Sure this is not a problem. As long as you site works and redirects to the right pages there is no harm in doing this. You might also want to use it for protecting your wp-config file from hackers by adding this to your .htaccess:

<Files wp-config.php>
 Order Allow,Deny
 Deny from all
</Files>

Good luck 🙂