The question in the Title is a set-up. The answer is no. And yes.
Deep-section carbon fiber wheels are no faster than their alloy shallow-section counterparts… at certain speeds. And therein lies the rub.
Let’s make a few things clear here. As my buddy, Chuck likes to say, I don’t know everything there is to know about cycling. To the contrary, I like to stick to what I do know and what I’m about to get into, I know. The Venge shown in the photos above has 17,000 miles on it – all on exceptional shallow-section wheels. I have another road bike and I’ve got more miles on it, all with shallow-section wheels:
All told, in the last seven years or so, I’ve got over 50,000 miles – all on regular, plain old, ordinary alloy wheels.
I wrote a post the other day, an initial review of my new Ican 38mm carbon fiber wheels. A commenter asked:
I do wonder, given your saddle time and the number of miles you put in, what you notice about speed with these wheels vs others. Specifically, I’ve been told the deeper-section wheels tend to hold speed better, therefore making the overall ride faster (less effort to maintain speed). Have you found this to be true, or what thoughts do you have on it?
I had heard, from maybe a half-dozen friends, that the deep-section wheels absolutely tend to hold their speed better, saving watts, but there’s a catch. This real, but magical power only kicks in at about 21-mph. In other words, the only benefit at 18-mph is style watts. In fact, I would argue against deep-section wheels unless you’re planning on averaging north of 20-mph because you’ll get killed with crosswind.
So this is how I know this: having put 50,000+ miles on standard alloy wheels, then jumping to 38mm CF wheels, I know what 25-mph feels like on alloy wheels. Better, I can describe it, because I’m geeky enough to have paid attention. As your speed increases, the resistance to pushing the air around you increases exponentially. You can feel this in the pedals – you simply have to keep pushing harder to keep or increase speed as you pass 21 or 22-mph (35-km/h). With 38mm carbon clinchers, you hit 21 or 22 and it feels like 20. 25 feels like 21 – and it’s an all of a sudden thing. You’re cruising along, expecting to have to pedal a little harder to increase your speed, and the bike just goes. If I had to guess, we’re talking about maybe 15 or 20 watts difference, but there’s no question you’re not pushing as hard to keep the bike going as you would have been on shallow-section wheels… and I’m only cruising on 38’s. I’ve heard the 50’s, 60’s, and even 80’s are even better.
I chose the 38’s for two reasons. First was weight and second was crosswind. I wanted a good all-around wheel rather than something that was just good on non-windy days, so I gave up a little on flat-out aerodynamic performance for a good cross between weight, aero performance and performance in the wind – because we get a lot of that here. I’ve got a couple of friends who run 60’s and 80’s (Zipp’s, both) and they get blown around considerably when the wind kicks up. Sometimes it’s even scary riding in a group with them, and they’re both exceptional cyclists. I didn’t want that. The weight was more a vanity issue, really. I wanted something in the 1,400 gram area (no tubulars – too much work) and the 38’s fit the bill nicely.
So, carbon fiber vs. alloy? I’ve got a good buddy who runs 32mm Rolf alloy wheels that are almost as light as my 38’s (75 grams heavier). Is a mere 6mm going to make a difference? I really don’t know, probably a little bit, but not enough to shake a stick at. Where the carbon fiber gets sexy is in the ride quality over the alloy. Most serious cyclists will know the difference between an aluminum frame and a carbon fiber frame. The difference in wheels is just as stark. So you go from an alloy frame to a carbon fiber frame and you’re a happy camper. Then you go from an alloy wheel to a carbon fiber wheel and you’re like, “DUDE!” And I’m like, yeah, I know. Because now I do know. It’s nice.
Here’s the important part: I can do things on my carbon wheels that I can’t on my alloy wheels. I’m just that much (pinches two fingers together so there’s a sixteenth of an inch between them) faster at higher speeds that it takes me from “strong cyclist” to “animal”. I like “animal”.
If you haven’t jumped on the bandwagon yet, if you’ve got the cash I recommend it.
UPDATE: Bucky added, “I think [a] point you missed is the effect of terrain (ride style). Enve have a nice graph on their website that shows that, for example, I’m hardly ever riding flat [roads], [so] I [don’t] need anything deeper than a 45mm rim. And some  say, I would actually be better with a shallower profile. Glad you love your wheels.
I find that reasonable enough, though I believe 50’s are the generally accepted “middle of the road” to tackle most terrains. I could be wrong, though.