Oh yes, I think everybody has some lightning protection on such equipment, if not a bunch of protection but simply put, it is not a failsafe. A direct or near direct hit can still destroy equipment. It was described to me sort of like bullet-proof glass. The glass might deflect the first round but you had better duck because the second round is coming through with the broken glass. In other words, lightning protection helps but anything close to a direct hit still gets through.
Insurance is fun. After months we got a tiny percentage of replacement cost after our primary transmitter took a lightning hit and simply had to be replaced. I think it was about 4 months after the new transmitter was installed that we got the check.