Q:

Can data model be changed in CloudKit after App is in App Store and Container is in production mode? 

What happens if I figure out I need an other entity in CloudKit and container is already operational, people are using it? 

A:

During development, you can make any changes you need.  When you deploy to the Production environment, Apple warns you:

After the schema is deployed, you won't be able to remove Production
  types or attributes in Development. 

So you can add types and attributes, you just can't remove them.  You can also add and remove indexes.