What you ride will depend on what racing you're planning to do. Flat time trials are very different from road races or etape type rides with other riders, downhills and corners. Apart from aerodynamics and weight there are some other factors to consider:
- Braking - what do the wheels brake like in the dry or in the rain?
- Wear - Will your investment last? For example, do their brake tracks wear out quickly if covered in grit?
- Robustness - is it likely that the wheels will fail? If they do, will the failure be controllable, and will it impact just the result of the ride or your safe completion of the ride? How easy is repair?
- Aerodynamics - is the wheel aerodynamic or not? I think you can sum up the aero test results in 3 factors: Most important is rim depth, then comes rim shape with toroidal rims being better in cross winds and finally fewer spokes being the least important factor. One should also ask whether you're going to Hawaii, Lanzarote or the Netherlands. Whether you need to ride in strong side winds and how good a bike handler you are should influence your choice of wheel.
- Weight - very much at the bottom of the list as differences are small in comparison to the system weight.
- Rigidity / Comfort trade off - I don't buy this argument. In my view more rigid wheels allow the bike to handle better and if you want more comfort you should deflate your tyres by 5psi and get a new pair of shorts.
So for flat, short distance time trials I think you're right in choosing a deep rim carbon front and a rear disc. A rear disc cover also sounds a good idea and in my experience they work very well for very little cost if they are allowed in the races you're planning. For general competition and training use, the relatively unexotic Vectors or Bontragers would be my choice. For something a bit more exotic I would rebuild something like a Mavic Cosmic or Cosmos rim (reputedly bombproof and widely used by Belgians for cobbled racing) onto a wider rear hub. Final alternative would be some specially made Lightweights. They would win any my tandem is cooler than yours contest.
In my view, a straight from the packet Kysrium isn't the right wheel for a tandem. The rim is not exactly aerodynamic and despite roadie beliefs they aren't much lighter than a good set of handbuilt wheels.
I don't understand why anyone would get a custom tandem in 130mm spacing unless they are going to run a disc 100% of the time since the literature on wheel strength being related to spoke bracing angle is quite clear. Rebuilding a wheel onto a wider rear hub is very cheap in comparison to broken spokes, ruined rides and possibly ripped clothing.