Hello,
in short, a "node" in Alfresco is basically a generic term for all kinds of objects in CMIS (can be document, folder or item). Every time you upload a document, create a folder etc. you are creating an Alfresco node. If you are only using CMIS to talk to Alfresco, it's better not to worry about nodes at all and stick to the CMIS vocabulary.
A site in Alfresco is just a special type of a folder, so you could create a new site via the createFolder operations in CMIS using the CMIS type "F:st:site". BUT: It is not recommended to create a site via CMIS as this will not initialize a site properly - for a site to be fully useable in Alfresco, there are secondary operations that are required (create roles, page and dashboard configurations, setup permission) that are not handled via CMIS.
Currently, there is no definitive way to support creating a site via CMIS. All potential solutions require that you prepare your Alfresco system somehow so that it automatically performs the missing steps when you do a "createFolder" operation with type "F:st:site". E.g. you could write a policy / rule / action in Alfresco that automatically performs all the secondary operations to make the site fully functional.
Note: The Alfresco Public API in version 1.0 does not yet support site creation as well, but this may very well be a feature that will be added in future versions.
Regards
Axel