The only bad thing about doing the bulk downloads is the way they name the files and you don't have the opportunity to rename them. A lot of them just have numbers. Once they're run through Calibre, of course, the names appear.
Would you recommend I download them in other formats like Mobipocket (I might get a Kindle one of these days) just in case
I wouldn't. I really don't see the point if you're using Calibre.