The forces that act on them are different and their masses are different so the books have different acceleration
This is wrong logic. Remember Newton's 2nd law $\sum F=ma$. If both the total forces on and the masses of two objects are different, then that doesn't imply that the accelerations are different. One could easily have double the force but half the mass and thus have the exact same acceleration as the other.
And this is exactly what happens and what $f_s$ takes care of on the top book in your example. Had its mass been larger, then it would be tougher to induce the same acceleration in it as that of the bottom book. Then $f_s$ would increase the total force in order to accelerate it just as much. But in the constant-velocity situation with no acceleration anymore, the $f_s$ doesn't have to worry about that - it only takes care of the air resistance which is unrelated to the mass.