The original question was asked in 2012, when almost all road bikes had rim brakes. Of the wheel manufacturers/builders the OP identified, one (November Wheels; disclosure that I'm a customer) builds mid to high end off-the-shelf rims and hubs; in the former case, anyone could buy the rims and build them up, and possibly even rebadge the rims under their own branding (with consent from the manufacturer). Boyd (disclosure, I have a pair of rims from them) has their own rims made in the Far East (I believe the profiles are proprietary). I'm less familiar with the other two, but I'd assume they operated similarly. In contrast, higher-end wheel manufacturers (e.g. Zipp, Enve) design their own rims and have them manufactured. This may be at their own factories (Enve), or they may have an exclusive arrangement with a factory.
All else equal, higher-end wheels may have more complex rim profiles, and they probably have access to better computer design (e.g. computerized fluid dynamics simulation) and wind tunnel or other field testing. Lower-end rims presumably go through less intensive development. I don't have any specific knowledge of this, but I wouldn't be surprised if they copy (either wholesale, or modify slightly) the profiles from other established wheels. As road wheel design has evolved, I don't think that the aerodynamics for a given depth are materially better today than 10 years ago. However, modern profiles are likely to be more stable in crosswinds. That might inform your selection between a high-end manufacturer and a lower-end seller using off-the-shelf (sometimes called open mould) rims.
Selecting among different off-the-shelf rims is harder. You can comparatively test wheels using the Chung Method of field testing, if you have an accurate power meter, a speed sensor, and some time and technical inclination. However, this involves getting your hands on the wheels, so testing many of them probably isn't practical. There are some more basic criteria you should focus on first, particularly internal width. This affects the actual width of your tires. In particular, 21mm internal widths are aerodynamically optimal for up to a 25mm road tire. In the road context, 23-25mm internal widths will be aerodynamically optimal for a 28mm tire. If the tire is too much wider than the rim, it will increase the amount of drag. (The magnitude of this effect is probably modest, maybe in the range of 5-9W at 25 mph, but I'm basing that off memory from various podcasts like Marginal Gains.) Many gravel wheels are gravitating towards at least a 25mm internal width, so that might also influence a buying decision.
And naturally, you can also ask about weight. I can't exactly recall what the situation was in 2012, but I think that modern road wheels don't focus heavily on low weight except at the very high end. In part this is because we've had experience about how light you can build a durable wheel. Also, we now know that weight has relatively little effect on performance.
Rim depth is the key parameter that influences weight and aerodynamics. In my experience, roadies will probably select up to a 50mm depth, sometimes 60mm, for general use. Crosswind stability is one thing to worry about. And in general, the deeper the wheel, the less stable it will be in crosswinds. However, there are two aspects to crosswind stability. First, a bigger surface area means you get pushed laterally. Second, each rim has a center of pressure relative to the hub. Crosswinds will produce a steering moment, and I believe that this is much more unpleasant than just being pushed laterally, especially when it's a gust of wind that you didn't expect (and suddenly you feel like the bike is making an uncommanded turn). This 2014 blog post by November Wheels discusses that concept. As mentioned above, however, with increasing development, even the off-the-shelf rims have increasing crosswind stability. For the same amount of side force, lighter riders should be more disrupted by a crosswind or gust than heavier riders, so lighter riders may have some reason to prefer shallower rims. However, we also produce less power than heavier riders on the flats, so this might counteract that preference.
I don't know how much aerodynamic drag differs between depths. The amount of difference might not be enormous. For example, Flo Cycling's 49mm rim brake wheel claims to take 20.50W to spin at 22mph with a 25mm Continental GP 5000 tire, versus 19.78W for their 77mm deep wheel. The difference between something in the 50mm range and something closer to 35-40mm deep might be larger, however.
