Welcome! This is a great question.
Prepare for a long answer because I love this topic
Obviously DT isn’t built as a book reading app, so other apps that are dedicated to this are in some ways shinier (smoother page turning interface, scalable fonts, etc.). But, DT is fine for book reading and actually I do a lot of my reading in DTTG nowadays, just because it’s easier to have my notes where I want them and life is hard enough without having to remember where you’ve put things and which app does what
As others have noted here, DT can’t handle dedicated book formats (also, you should be aware at the outset that Kindle’s format is proprietary and does not play nicely with other systems). However, with a bit of sneakiness you can convert most books to pdf, which is what I do. I do this for lots of reasons, but a key one is because pdf is highly compatible with other systems and I never have to worry about losing access to books I’ve paid for.
This forum isn’t the place to talk about how to circumvent pointless copyright laws that penalise readers, but if you want a set up like mine I recommend you have a look at an app called Calibre and do some reading about the optional plugins for getting Kindle books converted to pdf Calibre’s actually a great little app for managing digital books and I’ll touch on it more in a second (top tip passed on to me from someone online which I will now share with you: don’t download the latest Calibre update as soon as you notice it - always check that someone has tested the plugins you use and update once you’re certain everything still works).
Once you’re set up, it takes maybe 5 mins to buy a kindle book (or other digital book), convert it to pdf and move it into your database, and you’re good to go.
I don’t put my entire digital library into DEVONThink. I did try it (even though we are warned not to use DT as a junk drawer), but it will mess up your searches and you’re just making life harder for yourself when you’re trying to find something specific.
I keep my books in Calibre’s “library”, and I’ve put my Calibre library on iCloud. Calibre just uses Apple’s native file system to store all your books, inside one folder. It’s dead easy to navigate and if you stick it in cloud it is accessible from any device. When I want to read a book, I copy it to DevonThink.
I read and highlight in DT, and when I’m done I summarise my highlights as markdown using DT’s nifty function. I then go through this file and tidy it up and add any comments, then I file it in the relevant place in my database. I then move the highlighted pdf back to my Calibre folder (outside DT). This means my Calibre library has two copies of a book: the unmarked “pristine” pdf and the pdf with my mark up. (It actually has 3 versions of a book because I keep the original unopenable kindle file too but that’s neither here nor there!).
When this is done, I have in my possession a clean pdf of the book, a pdf with my annotations, and a markdown file with all my highlights and comments that’s in my DT database and searchable at any time. Life is good
[As an aside, if you read just in Kindle, you can export your highlights as markdown using the Bookcision extension, which is worth doing if you’ve got book highlights trapped in Kindle that you want to get out. You could just read in Kindle and always do this. I don’t because the problem with this is the highlighted book is trapped in Amazon’s ecosystem. In my setup, if I want to find a thing I read in a book and it seems I didn’t highlight it, I can just pull the book back into DT and run a search.]
Please ask if you have any questions. My current set up was a result of me asking lots of questions of Mac users who kindly shared their processes with me, so it’s nice to “pay it forwards”!