OK there is a workaround.
Firstly you cannot directly use iTunes to maintain your ebook library any more. Thanks for buggering that up, Apple.
And for those who said download directly from ibooks, YOU CAN'T - unless you have purchased the books from iTunes in the first place, which was NOT why I asked the question.
SO... I have found 2 workarounds, neither elegant but they do work.
Method 1: For epub format books into ibooks
1. First locate the book file you want to transfer using Windows Explorer.
2. Attach your iPad to your PC
3. When it appears in the iTunes sidebar, drag the book file onto the sidebar icon for your device.
4. It should transfer and be available to ibooks.
This is, of course a bit unwieldy for lots of books but it does work.
2. Method 2 for kindle.mobi format books, using dropbox and the Kindle app.
1. In Dropbox, create a books folder.
2. Put a copy of the books you want to transfer in the folder.
3. On your iPad, open the Dropbox app and open the Books folder.
4. Click on one of the books, it should download.
5. Click the export button (a square with an arrow pointing up out of it.
6. Click Open In... Select Copy To Kindle.
7. Kindle app should open with the book ready to read.
Unfortunately this method does not allow your reading position to sync across devices, but aside from that works well.
Feedback on this and any improvement to this or alternative methods welcome.