CMIS is a generic implementation and provides a common set of services to interact with any repository. It does not provide implementation for all the services specific to one particular repository. It tries to cover all the basic common services required for interacting with any repository hence it could be used generically.
Webscripts are the RESTful API supported by powerful alfresco webscript framework to interact with alfresco repository. Javascript based webscript allows the Alfresco JavaScript APIs exposed by alfresco to interact with alfresco repository. Where as java backed webscript allows to access all the services provides by alfresco.