I'll try and give you an answer to your questions, I hope this makes sense.
1) Control is returned to the user immediately. You need to check the status of the ID (DCMT D ID) to see if it has completed. If the ID is not found, it has completed. If it is found, that would indicate that the something is preventing the quiesce and IDMS is waiting. In your case, it will wait 60 seconds before forcing the quiesce by terminating the tasks or sessions preventing the quiesce.
2) It's hard to tell you which areas are "used together" . It might be all areas that fall in all SEGMENTs listed in a DBNAME, or it might be individual SEGMENTs, or maybe it's subsets of areas defined in a SEGMENT. It all depends on how your application uses the database and how everything is setup.
It would make sense to quiesce all areas that are in your backup.
Usually different DBNAMES point to different databases or different copies of the same database, but not always. Sometimes different DBNAMES end up pointing to the same database copy. It all depends on that mapping. Note that database names don't have to be in the DBTABLE as every SEGMENT is a database name in its own right.
Usually every copy of a database would need to be defined in a DMCL, unless it is a backup copy. That being said it is possible to use DD NAME overrides in local mode JCL to point to different copies of the database files, so it is possible to use a copy that isn't specifically defined in the DMCL.
There is no single way to do things in IDMS which makes questions like this difficult to answer.
3) Quiesce points aren't stored anywhere, though as you noted they are written to the job log, as well as the IDMS log. Exit 38 is invoked, so it is possible to use that to record them somewhere else or trigger some action.
Hope this helps.