The apparant weight may be less in water, but if the rocks sink, they are more dense than water. The total net force = weight of rock less the bouyancy caused by the displaced water.
Mathematically this is given by:
Net Force = g * V * (density rock - density water)
g = acceleration due to gravity, 9.8 m/s^2 or 32.2 feet/s^2
V = volume of the rock
If the rock is more dense, it will add Net Force downward, in addition to the tank water.
Imagine a rock with density 2000 kg/m^3, water is 1000 kg/m^3, and just to keep the maths simple, image the rock to be 1 m^3 (that is one huge rock, but just for simplicity). And lets take a tank of 10 m^3.
So, this 10 m^3 tank weighs 10m^3 * 1000 kg/m^3 = 10000 kg
If you put in the 1 m^3 rock, this displaces 1 m^3 of water, and assuming the tank only hold 10 m^3, that water is gone, out of the tank, leaving 9 m^3.
9m^3*1000kg/m^3 + 1m^3*2000kg/m^3 = 11000 kg, much more than the tank with waster alone.
So, rocks will add to the weight of the entire system.
The weight times the acceleration due to gravity is the total net force downward, so with the rock the net force is also greater.
The pressure of the water, the force per unit area is g*(tank volume)*(denisty of water)/(area of tank bottom). But, since water is a liquid, the pressure is equal at all point on the bottom of the tank. This is how the manufacturer knows how strong the tank much be... the tank has to be strong enough not to break until the water putting this amount of force on the tank.
If you put a rock in there, on the bare bottom, it most likely does not sit flat... it will sit on its points. At those points where the rock hits the tank, it will spread its entire weight -- its entire net force from gravity - over just those points. So, where water will spead its force out, the rock concentrates it force, and it may be too much for the tank to hold. This is why gravel and sand helps a lot, since if the rock sits on them, it speads this concentrated force out, not unlike water.
So, in answer to the original post, I think so long as you do not put too many, and set them on top of your substrate, you should be fine. You can always calculate the forces on your tank walls and bottom and then ask the manufacturer what the maximum is.
So, sorry for the long post, but be careful not to confuse weight and mass and density. And to summarize, if the rock sinks, it is more dense than water, and the total weight of the entire tank and its contents will increase.