I have clearance issues running cantis and a rack. Wondered why my braking had gone rubbish, then realised the little metal Dairylea on the straddle wire was hitting the rack struts way before the pads contacted the rim.
I get mild brake judder too which nothing seems to cure. I notice that Mick is running his straddle wires really high which might help, but it also makes your brakes a lot less progressive and powerful.
The reason that CX bikes come with cantis is to do with mud – clearance thereof, and the stuckness of the UCI regulations therein. Nothing to do with performance IMO.