Hi,
I would think that even if it does not resonate it is still something to think about.
I always say that more data is better than less data, as long as it is well organized. I think they did a decent job in the pdf. I thought about similar things in the past because i started using big fans to cool my computer case guts and i wondered about the effect on the +12v line. What happens when we turn off, there must be some inductive current coming from the fan, and if it is enough it could charge the filter caps up to some level which would have to be determined.
I thought about suggesting a series inductor similar to what dr pepper said, but as you know before you can insert an inductor into a circuit you have to know the effects during any and all modes of operation, which includes turn on and turn off, so you cant just stick an inductor in between the P/S and the fan or the fan could be destroyed on the first run.
It's also very hard to design an inductor capacitor filter with a single inductor and one capacitor without knowing the detailed dynamics of both the source and the load. It might be possible to cheat here by using a pi filter, but that will take decent sized caps too.
So the only thing left is to use a lower voltage fan and use a regulator circuit to regulate the voltage or maybe the current. It would be operating in the 'limiting' mode so it should not have to store any energy. Unfortunately this will act like a largish resistance so there will be power loss. But that's life. If you are not allowed to store energy then your only choice is limiting. Think about this for a while. Also, added series resistance decreases resonance as the damping factor is altered.
A 36v fan that draws 0.667 amps will cause a 12v drop in voltage with a 18 ohm resistor in series with it, and the resistor will dissipate 8 watts, so the efficiency will be 75 percent in driving the fan. 32 watts in with 24 watts out means instead of the power supply powering 24 watts it will have to supply energy to power 32 watts. It's a loss but that's life. Of course you need to test this as well.