Yes, the fan is just connected to 5V and always on at full speed. We had some PWM speed modulation hardware logic on a previous version of the board, but that one had other issues, so finally we decided to roll back the design for mass production.
Making a guess based on CPU usage is the best. Anything below 300% should be no problem using a large heatsink like we used in that doc page you mention. We had a deep net running at 375% CPU (i.e., almost loading all 4 cores to the max) and that was stable with the heatsink.
I see DemoArUco around 220% CPU in the screenshots here: http://jevois.org/moddoc/DemoArUco/modinfo.html
So it should be no problem. Make sure you have a good thermal contact with the heatsink. You may want to spread the glue on the chip with a screwdriver or such so that it fully covers the whole chip before applying the heatsink.