Moving my main business ecom site to a dedicated server. The way the dns will be set up will make ns1.mydomain.com the primary server name. I will be hosting other sites non related to my ecom site on this server (my web design clients). If I understand correctly all additional sites on this server will have ns1.mydomain.com as there primary name server for dns setup. Does this in any way harm my ecom site? Search engines or otherwise?
As far as I know it shouldn't have any detrimental effects on your site. A company I was at once has two name servers and we hosted several sites on them along with our own. Our site always did fairly well in the search engines as well.
This will in effect result in all your domains being hosted on the ip address (or block) - this will/could affect your rankings in some search engines (ie. google) if your sites are relying on links to from each other for there PR. Meaning - a link from a domain that is in the same IP block as your own is not as valuable as one completely unrelated.
I recommend posting a query in google asking if multiple sites on one IP will cause problems to get the SEO experts to look at this ;) DNS is such a turn off.
By the bye - most of my sites are on one IP - a virtual hosting package - so probably lots of others too. I haven't noticed any problems with links being ignored, sites not being indexed etc etc, even when the only link in existance is from my site ;)