I split omnibuses because I like to have one file per book record in Calibre and so I can mark them read/unread individually. To be fair I also have a record for the omnibus as a whole and I could have "empty book" records for the individual books but it's not the way I work.
Plus, in my limited experience of about 4 cases, the omnibuses are sometime very badly put together. Whilst I agree that no modern reader should barf on size alone, my Kobo Touch gets cranky if the individual files within the epub are too big. One particular omnibus I had - a complete works of HG Wells - had made each work, including the novels, a single file. It was also an opportunity to tidy up the formatting which was atrocious.
Having said all that, my Kobo Touch is now my least used reader.
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