I said in iOS 11 Thread:
Annotating PDFs in iBooks works well, once you get used to living with the bug that the button that brings up the annotations functions disappears if you switch to a different app while you have a PDF open in iBooks. The only solution appears to be closing the PDF, quitting iBooks, re-opening it, and then re-opening the PDF. That it doesn’t remember which pen, colour, font, text size, etc. you had selected if you close the PDF is a minor annoyance relative to the whole button disappearing.
Though I haven’t tested exhaustively, it looks like this got fixed in 11.1.2, at least.
Edit: Or maybe not, some more testing showed.