The term "custom DNS server" refers to the name servers which you are using being branded by you instead of reflecting your host�s domain name or a generic name. Instead, you use a domain name of your choice. Resellers should use custom DNS servers in order to brand their services and to hide the fact that they are receiving hosting from a larger company. It also makes moving to a new hosting company very easy in the event of problems.
There is no reason why you should not use custom DNS servers. It can even help you to find new clients. If anyone does a whois lookup on any of your client's domains they will see ns1.YourDomainName.com and might visit your site.