what
cybmole says
I synch my 2 data drives daily, totalling about 2.2TB of data. Logs indicate typically 1-2 minutes to Analyze a drive, and less than a minute to Synch a drive. I normally do it in my shutupShop script, so for me the time taken is zilch.
A disadvantage of format specific libraries is if you add a column or change some metadata on your EPUB library then you must/should/could do the same on your MOBI library.
BR