I've had a Jandy Aqualink RS system controlling my pool and spa for over 12 years. Twice during that period, a (very) nearby lightening strike has knocked out the RS-485 comm between the main board and my two indoor controllers (one, a real Jandy RS; the other, a RS-485 to RS-232 converter from the same company mentioned below) and by "knocked out", I mean that it "fried" something on each device (visibly on the indoor controller in the form of a burned surface mount device). Both times, I got used replacement boards from eBay, but it's still a pretty spendy proposition, plus the converter is another $70.
After doing some research and briefly considering installing the "official" Jandy surge protector (I rejected that idea since it only claims to protect against power surges, not lightening), I decided to go with a different surge protector. I used the 485HESP from B&B Electronics, placing one between the wire and indoor controller, and one between the wire and main board inside the power center box. These units are $109 each, but if they can save me from having to buy more equipment, it'll be more than worth it. I also employed the services of an electrician to install them as there were grounding concerns and, well, it was only $90 and sometimes it's worth that to not have to hassle with it myself.
I didn't take photos (didn't think about it until afterward), but the indoor unit was installed in the wall behind the Jandy controller (before the wire splits to go to my RS-232 converter), after basically cutting out a big enough hole in the drywall to fit it in. Ground was available there from a nearby light switch. In the power center, the device was installed in the bottom of the box below the relays, and grounded to the ground bus bar that was already installed. The system started normally on the first try after buttoning everything up.
So, I guess I won't know if it worked until we have another big lightening strike, which, of course, I hope never happens. I'll update this thread if I have any more info (good or bad), but for now, at least I know that the approach works for what us software guys call the "happy path". Hopefully I'm protected from the other as well.