Obviously - intelligence costs.
Echopraxia (and prequel Blindsight) present ordinary, baseline humans dealing with entities far smarter than they are. It's a hard call for the author: are his super-intelligent beings smarter than the author himself, his readers? How then can they possibly be imagined?
Try another question first. What possible utility could super-intelligence have in evolutionary terms? After all houseflies, not known as paragons of smartness, seem to have had no problem colonising the planet. The answer has been known for a long time: in a predictable environment (aka ecological niche) the organism can get away with hard-wired reflexes - instincts - and that's the way to go. Intelligence is the way animals deal with problem-solving in variable, somewhat unpredictable environments, often when they are social creatures and have to compete with equally-complex and hard-to-fathom conspecifics.
Still, we are where we are and there's not much sign of super-intelligence in the myriad species inhabiting this globe. So what are the fictional super-smarts actually doing?
In Blindsight/Echopraxia they are capable of maintaining and manipulating multiple highly-abstract models applied to extrapolating from the current situation. They understand what they perceive at a much deeper level and can predict and direct consequences far better than we can. This assumes of course that these deep levels of abstraction are actually relevant: a quantum physicist understand the dynamics of the world far more profoundly than any lay person but in everyday life it makes no difference - and even gets in the way.
To be super-intelligent in a way which pays off you have to be in a situation where complex phenomena are directly causally present, and you must possess super-senses and super-tools to act effectively on your superior understanding. In Echopraxia for example, most of the super-smarts are able to perceive and affect human brain states directly, and manipulate effective theories of human brain functioning in real-time. No wonder they run rings round us. They have a similar relationship to advanced technologies, which makes them pretty effective in dealing with power and transportation platforms and weapon systems - always useful in an SF novel!
The moral is that being as stupid as possible (but not stupider) is the right answer - but the ratchet of that minimal level keeps cranking up, as science and technology complexify our environment.
So how does Peter Watts convey to us, his readers, the super-intelligence of his protagonists? By making his stories intricate puzzles where we're never quite sure who's doing what to whom, and why. After the novel is finished, you reflect, try to make some sense out of the hints, the apparently purposeless or perverse actions. And then it starts to come together: being slow-witted is sometimes homologous to cranking down the clock speed of the very smart.