When Illustrator saves things it makes a PDF file out of your artwork (yes, the AI file is a PDF by default). Illustrator then embeds its native data into this PDF file. The result of this is that Illustrator needs to save one version of the effect flat rasterized as PDF cannot have live effects.
You can disable the PDF embedding by unchecking the 'make PDF compatible file'. When you do so Illustrator produces a MUCH leaner file, partially because data does not need to be stored two times. Of course, this assumes you didn't permanently rasterize stuff. Some applications such as InDesign won't like this though, so you may have problems with those files outside Illustrator.