Yes. I agree that at the end of the day it seems BETTER for devonthink not to work with epubs. It is annoying and time consuming to have to use calibre for the conversion but it is done only once. And then I agree: PDF is a better format for storing annotated documents.
So, I ended up storing both pdf and epubs in my DB but using only the former. The only issue is if I want to read stored epubs in an iPhone or iPad mini - then epubs are handy. iBooks will NOT open without internet, even if the pdf is already stored. I found an alternative: TI-READER. It seems they are not updating it anymore but it works great for now. Just wanted to share. Thanks to all of you that commented!