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I think Kindle is the same as Kobo - there's no sub-collections, and no tags. So your Calibre tags will need to match your shelves/collections (or drive the shelves/collections).
My Calibre tags are either Genre or Sub-genre, collections or ebook management tags:
*Ebook management tags don't get transferred to the device, but others do.
*Collection tags will also have a Genre or Sub-genre tag, and the collection tag forms a shelf on the device. These are either books I need to prioritise reading or are length-based (when commuting I read short stories or anthologies as they neatly fit into my train journey).
*Genre tags get split into Sub-genre tags when there are more than around 300 books.
My suggestion would be to start by defining your collection in terms of genre - think of how a bookstore organises books. Keep the categories fairly broad to start with, then split large groupings into sub-genres. In terms of collections/shelves on your device, I would try and keep that number reasonably low - you don't want to page through multiple pages to get to the collection you want; I currently have around 50 shelves on my Kobo and I need to split out my SF collection into (more) sub-genres.
I can post my Calibre tag/shelf list if you like, but it's somewhat idiosyncratic.
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