The biggest problem with double sided scanners are consistency. I ran my Super Nintendo manual collection through an Epson DS-510 and the results were ok at 600dpi, but the only reason I say that is because it has spit out 20,000 pages which would have taken an *eternity* with a flatbed. Maybe it was just the software, but some scans came out terribly dark. Also, if you get any gunk off a manual or dust specks, be prepared to rescan a couple hundred pages with a white streak on them (which I'm still finding those). Luckily this Epson does a reasonable job flattening out the spine. Perfect? No.
The other kicker is that if you do take the staples out and the pages apart, good luck getting them to re-align later after retouching the images. Image 1=back page,cover. Image 2=inside, inside back cover. Image 3=Page 20 whatever, Page 1. Your manual's inside facing pages are now stretched from image 2 left to image 3 right.
When I did do a bunch of flatbed scans, I ended up getting a set of these and trimmed to fit the edges of my scanner. Again, not perfect, but it was consistent across scans. Definitely still need to weight down the pages/covers (It's thin but not that thin), but at least you aren't loosing any off the edge.
http://www.amazon.com/Swingline-SmartCut-Replacement-Cutting-9212CM/dp/B003DW94AY/ref=sr_1_12?s=office-products&ie=UTF8&qid=1426967821&sr=1-12&keywords=%22cutting+mat%22
