Of course, in calculating the efficiency and production of solar water desalination along with the collector, the area of the collector should be included in it
The efficiency of solar desalination system usually includes the amount of solar irradiance that falls upon the solar collector. The only way to properly calculate the total irradiance solar collector is by calculating the area of the solar system.
However, you can also defined the efficiency is specific terms which is W/m^2, this would also work depending on the aim your research and how you conduct you math model. In this case, the area is not necessary. in this case, you output needs to be in specific are terms which is (water output/m^2 of solar area collector).
Efficiency is a unit-less ratio, so the most important thing is to ensure that the output and input are of the same unit for a proper efficiency calculation.