Ciao,
The REST API are more flexible because you can extend them writing a simple webscript.
The CMIS API are less flexible, but can be used to develop clients that are "vendor neutral": the same client can access different CMS.
Your second question is not clear.
The unique ID created by Alfresco is not always the enough. For example if you export a folder as an acp and then you import the acp, even in the same repository, the UUID of the nodes will not be the same.
It is always better to associate to the documents an ID that is saved as a custom metadata.