I was reading a paper on the theory of magnetic water treatment just the other day. Quelle coincidence.
The effect is currently not well understood, but there does seem to be a reasonably large literature built up over a fairly long period of time testifying to its effectiveness. The exact nature of the effect seems to be a little vague, however. The main effect is generally:
i) reducing scale deposit or
ii) producing a less tenacious scale
In a series of papers beginning in the late 80s, Dalas and co-workers looked at the following techniques for retarding calcite crystallisation: magnetic fields, ELF electric fields, UV radiation and ultrasonic fields. They found that all treatments had an effect. The mechanism of crystallisation wasn't affected, but the rate constant was, i.e. the speed of the crystal growth, which suggests that some other part of the crystallisation process was being affected (e.g. removal of water molecules or migration processes).
In the paper I read, the authors pointed to other research which showed that particles of calcium carbonate and sulphate formed larger aggregates under the influence of a magnetic field. These larger particles tended to stay in solution rather than adhere to surfaces. They also provided sites for further crystal growth, as opposed to the surface that one would be looking to protect.
The authors suggested that two types of effects could be affecting the dispersion and crystallisation: first, that the magnetic field could be affecting the hydration of ions and solid surfaces; second, there could be Lorentz force effects on the ions and dispersed particles. The Lorentz force acts on an electrically charged particle when its passing through an applied magnetic field.
Which of the two effects would be important would depend on whether one had a static or dynamic treatment regime.
I am somewhat confused by some of the statements on that website, but this is not an area of expertise for me.