So the colour illustrations are specifically mentioned in the J-NC FAQ:

Note that the pre-pub versions may not contain all the illustrations found in the final ebooks, such as the color illustrations usually found at the beginning of the book.

For Bookworm specifically some other stuff not included are the maps (from Part 2 Volume 3 onwards there is a duchy map every volume, Part 3 Volume 3 through Part 3 Volume 5 there is a duchy map annotated with [Part 3] Jureve ingredient locations, from Part 4 Volume 1 onwards there is a map of the entire country), the character list, from Part 2 Volume 4 onwards the four-panel manga (these are mentioned in the volume descriptions), and the results of the character polls in Part 3/4/5 Volume 1.

Some of this stuff is at the end of the volume (which requires you to buy the volume) but some is at the start (like the colour illustrations) so you can see them by looking at the volume previews e.g. click Look inside on Part 2 Volume 3 and you can see the colour illustration, the duchy map, and the character list before the table of contents.

Now for other series if you buy the ePub directly from J-NC you might get other bonuses not in the pubs (list here).