You *might* have a problem on the wide end of the 17-40mm depending on whether you're using a full frame or a crop sensor body.
I use Cokin P and 85mm NDs & ND Grads on my 77mm filter lenses (Sigma 10-20mm f/4-5.6, Nikon 70-200mm f/2.8 VR and Nikon 300mm f/4 AF-S). With the 70-200mm & 300mm it's not an issue at all, works flawlessly.
With the 10-20mm, I can't shoot wider than 14mm before I start to see the filter holder in my viewfinder (although I'm using a regular holder, not the WA one). On a full frame lens, I believe you start seeing a regular Cokin P holder at around 18-20mm.
They can be a little prone to flare in some cases if the sun can catch the edge of the filters (basically you start getting internal reflections inside the filter itself), but there are hoods that go into the end of the Cokin holders to help with this (similar to matte boxes you see on movie cameras). You can cover exposed ends with gaffer tape, or make your own
French Flag type shade out of cardboard, like they use on video cameras.
So far my Cokin P investment is relatively small (about 60 quid total for the holder, 77mm adapter, 3 stop ND Grad and 3 stop ND), and it does have its issues on very wide larger diameter lenses that I've seen. It's far from useless, but I do intend to pick up the X-Pro Holder & 100mm filters at some point in the future for use on the 10-20mm.
As I said, on the 70-200mm and 300mm lens, no problems whatsoever.