Actually, National Geographic are correct to say that. Thermoregulation has long been posited as the reason behind gaping, and although it's likely that gaping has some thermoregulatory function it has not been proven, and gaping has other roles.
One study done on alligator gaping showed that gaping had no effect on brain temperature (the only feasible role that gaping has in thermoregulation is to cool the brain, not the body). This study was somewhat flawed, however, in that dead alligator heads were used - the role of circulation is therefore ignored. But in reality it's a difficult study.
But we know that gaping also has a social role - it is a low level "threat" signal that is commonly employed between individual crocs, and to other species (like humans who get too close). The bright white teeth and striking yellow tongue are powerful signals in crocodile-speak. Even we understand it! Once it escalates beyond this threat, other body movements and vocalization (eg. hissing) start to be introduced. But a croc lying on a bank with its mouth open is more likely to be making a statement about its territory than it is trying to cool off.
Gaping by cooling is most effective is fluid evaporates from the tongue, but the tongue quickly dries in gaping crocs, there is no active airflow over the tongue to facilitate evaporative cooling anyway (unlike panting dogs) other than natural air movements, and the tongue is relatively poorly vascularized. Evaporative cooling just doesn't add up. Gaping will provide a role for convective cooling, but nobody has proven this.
Other suggestions include angling the cranial platform away from direct sunlight to reduce brain overheating, exposing the tongue to UV radiation to kill harmful bacteria, and allowing birds to enter to tear off "hairy leeches" (as Herodotus put it). Perhaps gaping fulfills all these roles at certain times.
So while it's not completely accurate to say that nobody knows why gaping occurs, it is accurate to say that it's not simply due to thermoregulation.
Adam Britton