Great Questions -
Unfortunately 'refer to the online help' isn't the most descriptive, but that reference is to the revisions made to the 6.6 version of the 'ThingWorx Extension Development Guide' which is posted in the online help here: http://support.ptc.com/cs/help/thingworx_hc/thingworx_6.6_hc/index.jspx?id=ThingWorxExtensibility&action=show
The particular section inside the Developers Guide that will be helpful with the issue you are experiencing is titled 'Project and Extension File Structure'. This Section explains that the Entities xml (such as the StyleDefinitions, DataShapes and MediaEntities you refer to) for entities not associated with java code are being moved out of the metadata.xml and into their own individual xml files in a structure explained in the Developers Guide. Hopefully this makes it easier for Extensions developers like yourself to view, make revisions and add/remove the Entities from your extension without the headache. (It also facilitates the use of 'Export to Source Control' a new 6.6 feature in Composer that exports entities in the same structure).
To remedy the concern from your second question, we will continue to support all these entity types in extensions for the foreseeable future. The only thing that changed is the location of the xml that defines the specific entity.
Let me know if any of this doesn't make sense.