Why is the energy density of 26650 Li-ion cells lower than that of 18650 cells?
If we just compare the two cells you linked, there is an obvious difference: The 18650 is rated for 5A continuous discharge while the (twice as big) 26650 is rated for 20 A - four times more. 
The size of a battery is not only determined by capacity (energy density), but also by its current output (power density). The inner structure has to be built in a more massive way if you want to draw a high current from the battery which requires a low internal resistance.

If you check typical applications for these batteries the large 26650 is normally not used in applications that are designed for long running time but rather in those using a lot of power like high-end flashlights.