Originally, water boxes served the function of equalizing the water pressure to the pump, regardless of the pressure coming in from the faucet. The reduced the pressure to, in essence, no pressure. That way, the pump always had the same inlet pressure and chemical mixing, when used, was always the same. (This was because the pump pulled chemical only when slightly "starved". If it was being "force fed", it was not "starved" and therefore did not pull chemical.)
In some designs, the water box is basically a large heat sink. It protects the pump by, in essence, making the bypass much, much larger than a hose by itself would do. However, this is secondary in function to the above.
In heat exchange systems, the water box is actually a "heat reservoir / heat collector", instead of a "heat sink". In other words, it accumulates heat in order to increase system output temperature, instead of loses heat, in order to protect the pump. (There is a balance there, so it's not "either / or"... it actually does both at the same time. It collects heat. But it also protects the pump because of it's size, which causes the water temperature to rise gradually and not be as likely to suddenly "spike".
If you have a heat exchange system, replacing the water box is simply a mistake. It's integral to how the system works. And the system will not work as well, regarding heat generation without it.
In addition, some HX water boxes are "mix tanks". In other words, the cleaning chemical, if injected into the system (vs. being a pre-spray), is mixed in the box itself, or, just prior to the box, as the fresh water comes in, via a chemical injector valve (much like a HydroForce). Getting rid of a water box would also negate the mix capability that the box provides.
