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Both classic MOBI and ePub are compressed formats. You can't have an ePub without it being compressed. An ePub file is a special case ZIP archive. Classic MOBI files are encoded much like compiled programs. As Kovid mentioned, they are different compression methods that produce differing results. Also, the file structure is different and that will have an impact on file size.
mbovenka's point comes into play if the book contains images. The output profile you choose for conversion can resize and recompress the images leading to differing sizes.
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