I used a BOB trailer on my 5100 mile cross country tour. I rode with several different folks using the classic 4 pannier set-up and we did some non-scientific coasting tests to compare the wind resistance you described. In all cases, both frontal and side winds the BOB rig was better and that was me on a jumbo sized Cannondale frame, the largest they make with a mountain bike seat post so that I can get the seat high enough for me. The BOB packs more compactly and therefore presents a smaller frontal and side area for wind resistance. From the front, you bike has already begun cutting the wind which helps the trailer. Wind resistance is a tourists number one enemy.
If you have strong wheels you won't have a spoke problem with either set-up.
The down side to a BOB trailer, which is significant to many cyclist is the transport of the trailer to and from tour start /end points. Additionally dealing with an awkward 15 foot long (?) bike on a day to day basis can be a pain, especially for someone without the upper body strength to maneuver the heavy trailer. Every time you stop for a photo or at a store you have to deal with this trailer that never seems to be in the right position, try backing one up. I put a handle right on the BOB fender and have no problem lifting and moving it while loaded, but I'm sure that many would. I also put a second kickstand on the trailer which really helps in the parking department.
So pick which ever floats your boat and get out and ride.