They made this map by spidering public onion sites, so you're only seeing sites that were publicly linked to on a site they crawled. You could brute force the .onion address space to get a more accurate estimate of the number of onion sites currently online, but that would take a long time at the speed Tor operates.
The irony being that they made a map of the dark web which contains almost no part of the dark web because they couldn't find it. I, too, can run wget pointed at an onion ring network, and it would be just as unimpressive a result as this ...
