Back in the "old days"....
Fire and security systems used "relays" and were not prone to lightning caused false alarms.
Then they came out with the "transistor" and these are very sensitive to any little momentary "blip" of electrical contacts as well as lightning induced current in building wiring.
Relays, if energized, will remain closed for a moment upon losing power, then will open. The coil maintains its charge for a moment upon losing power and it takes time for the mechanical contact arm to disconnect the contacts.
Transistors on the other hand will activate instantly!
Then you have all that wiring running around a building acting as an "antenna" - all feeding into that sensitive transistor (integrated circuit chip).
Basically what happened with the introduction of transistor controlled fire and security systems was a ton of false alarms during every lightning storm.
One way to fix this is to isolate the building wiring from those sensitive transistors using "relays". 12 vdc running on the wiring loop powering a relay in the alarm box. Lose power to the relay, then the contacts from the relay then trip the zone in the alarm box. So basically the sensitive wiring is contained within the alarm metal box.
The only problem with this is the wiring is not "monitored" for a short or trouble condition as is done with an end of line resistor on the zone. This would monitor the wiring for a short or open for the entire length of the wiring if installed properly.
So the next option would be a "faraday cage" type thing. Use of shielded wiring throughout the building and the shields grounded at one end, should prevent induced current in the wiring from lightning.
Faraday cage...
http://en.wikipedia.org/wiki/Faraday_cage