Yesterday I read an Anki tutorial https://leananki.com on the web and he said that is better to save all cards in only a deck. You remember better when the questions are from different topics.
I think that is better to add the option to study from all decks together when you want. This way you can also study from only a deck if you want.
You already have two ways to study your whole collection:
Create a parent deck and make all your other decks children of it.
Advantages: Works just like any other deck, inactive decks can be simply removed per drag and drop.
Possible disadvantage: New cards will be fetched from the child decks successively (not randomly from the whole collection).
Create a filtered deck for the whole collection (requires the new scheduler).
Advantages: More options, complete randomisation is possible.
Disadvantage: More complicated to set up and use.