Mostly – because of your limits. You showed us one Options preset. If all of your decks and subdecks are using that preset, and use the preset’s daily New limit of 50, then those limits interact – The Anki v3 scheduler - Anki FAQs .
It also looks like your parent decks aren’t “empty” – they aren’t just folders that hold other decks, they (at least some of them) have cards of their own. And it looks like you have more subdecks than just 01-12 that we see in your screenshot – which is why the the top-level totals for Due and Learn (which are unlimited) are so far off.
If you want to know how many cards actually exist – not subject to the daily study limits of any particular deck – that’s what the Browse window is for. You can click specific sets of cards in the sidebar, or search up any category of cards – decks, subdecks, tags, card state, etc. – to see how many are in it.
Display Order in your Deck Options.
All the things you’re asking about are standard in all of the apps, so there’s no concerns there. Update your preset(s) in one place, and everything will sync with the rest of your collection.