Hi,
I understand that I need to read and mark up .mobi, .epub, kindle & apple books in their respective external apps, but I wondered if there is a way to import these files into Devonthink in order to have DT search the full texts of the documents alongside my PDFs and other documents.
Thanks,
Rebecca
DT is fine with DRM-free .epub files, but not .mobi or DRM-protected formats. But you can convert .mobi to .epub in Calibre, and DeDRM can strip DRM from older (pre-2023) Kindle books so that you can convert those too.
I don’t think you can move Apple Books out of their ecosystem at all (although I haven’t tried for several years) - the Apple philosophy seems to have been not to create a walled garden, but an entire prison for books 
Kindle files you can download and move, but as Nick has noted above, they are protected by DRM and are unreadable by non-Kindle programs unless you convert them to another format first.
I don’t use Apple Books at all (and for what it’s worth I recommend that others don’t either - it’s almost impossible to back-up or extract what you do in there), so can’t give advice on that, but for Kindle and other file types I personally convert everything to PDF and store that in a DT database that I have set up solely for that purpose.
I actually also keep all the PDF files in a second location in icloud as well as a “back up”, but most my interaction is via DT.