InDesign has a feature to export Epub files. However, these files are not usually publishable as is. Post-editing is necessary to clean up the format and restyle the file.
The most obvious issue is a lack of page breaks at chapters. This can be taken care of in Calibre, by simply importing the Epub and converting “from Epub” “to Epub.” Other editors do a nice job of this as well; I recommend a program called Sigil (which will be handled in more detail in a future post).
I highly recommend unchecking font embedding, as it is not supported by Kindle.
Images require some degree of attention when exporting. It’s important to note that Kindle doesn’t wrap images–they must all be in-line. Resolution is another issue. Using 72 dpi will usually look fine on screen, but to allow readers to zoom in and double the size of the image, 120 dpi is recommended. But if you have a lot of images, this rapidly becomes a very large file. Selling large files through Amazon becomes costly, so downsampling is recommended if you have very large files. For EXTREMELY large files (around 100Mb), you start running into the memory limit of the Nook. We have a book (Pictures from a Distant Country) that, at full resolution, takes 100% of the Nook’s memory.
For tables, many of them look terrible on e-readers. Often we simply convert tables to image files (jpeg) in order to prevent formatting problems.
Hyperlinks export well from InDesign and should be used within the text of a book destined to be an e-book.
For more details, I highly recommend the books by Liz Castro sold on her site. They talk about every e-book formatting issue and features and bugs in InDesign.