The first sentence pertains to a particular object. While the second implies all of it.

Also, what comes to my mind when you say "whole cakes" is something like whole wheat bread. :D

Whole cakes = entire cakes, meaning 100% of the cake was eaten. All cakes = every one of the cakes. You could have a situation in which there are 10 cakes, and the students ate 3 cakes fully. In this case, 3 whole cakes were eaten by the students, but not all cakes were eaten (there are 7 left)

The whole cake was eaten by students All cakes were eaten by students