I also count short stories separately if they've been published individually. I would also count a short story separately if I only read one story in an anthology (and if an individual entry exists for the story on Goodreads).
Otherwise, if I plan to read all or most stories in it, it would definitely be one collection/anthology = one book.
I read ten Doctor Who 50th Anniversary short stories last year - one per month, as they were released, as individual ebooks. So those counted as ten books. (I also read two ~1000 page books last year, for example, so I'm thinking it does even out over the year!)
With omnibuses, I split them up for reading, and count each one as a separate book - especially as I won't be reading them all after one another.
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