Here is my situation, I have an e-commerce site mydomain.com and my host only supports shared ssl certificates, they do not allow private ssl certificates. In order to easily keep the session going for the shopping cart on the secure server which is (secure) mydomain.hostdomain.com I am redirecting mydomain.com to (unsecure) mydomain.hostdomain.com as my sites address, which works fine. My question is will search engines have an issue with indexing or ranking a site address of mydomain.hostdomain.com?
Also, am I correct in assuming that mydomain.com is my domain and mydomain.hostdomain.com is a subdomain of hostdomain.com? I have also noticed that when I try to check my Alexa ranking for mydomain.hostdomain.com it only displays results for hostdomain.com
mydomain.hostdomain.com would be a subdomain you shouldn't worry about the search engine indexing mydomain.hostdomain.com because that's just part of the checkout process you want your homepage and product pages to rank well
The problem is my homepage is mydomain.hostdomain.com, because I need the session to stay the same when they switch to the secure server. Two different domains can't share the same cookies. So, when someone types in mydomain.com it redirects them to mydomain.hostdomain.com.
I know that mydomain.com won't get indexed, because I'm using a 301 redirect to mydomain.hostdomain.com. My question is, will google and others have any problems indexing mydomain.hostdomain.com? Would search engines index mydomain.com better then mydomain.hostdomain.com or does it not make a difference?
It makes a difference specially if it's a subdomain for a high authority domain name. However, search engine won't face any problems indexing your website content if it's mydomain.hostdomain.com