Something I have always wondered.
It's nice to hear you are thinking about the problem and not just reading something someone said and implementing that. Living in Tallahassee, you need to know this stuff, and implement something that works. Tallahassee isn't the worst place for lightning, but it's bad enough.
Thing is though the transmitter and a receiver both have an electrical 'safety ground', the third pin in the AC plug that bonds to the branch circuit ground which runs probably over 100' before it is bonded to its earth ground at the serving panel. This safety ground is typically bonded to the case of the equipment so that it in essence creates a long ground loop between the station ground and the ground at the serving panel. I believe the NEC says that bonding the branch circuit ground to the earth ground out at the shack is a no no but isnt that exacly what has been done?
Yes that's what NEC says. You are required to tie all the grounds together, ouside the house. Look at what how the phone line, water line, TV cable, and any other line you have entering the house, are grounded. They all have a wire running to the AC entrance panel ground rod.
I think the station earth ground should be bonded to the serving panel's ground but as I said its over 100 feet away and that would be yet another ground path.
That 100 ft wire would satisfy the NEC requirement, and probably be an OK ground at 60 Hz, thereby providing safety for 60 Hz faults. However that won't protect your house from lightning damage. With that 100 ft run, as you noted, there are now two paths for the lightning current to take, one thru that 100 ft wire and one thru the wiring inside your house. Those paths are in parallel and the lightning current will split between those two paths depending on the impedance of the paths.
The impedance of a 100 ft long #4 wire at 1 MHz in free space is about 360 ohms. Buried in the ground it will be less and it will conduct current to ground along its length, but it still going to be a large impedance. It's a very poor ground at 1 MHz (where lightning has a large component). The amount of lightning current you have in this wire depends on how the rest of the system is grounded, but when you start with a 20,000 to 50,000 amp pulse distributed over a very wide frequency range, you can assume there will be a significant amount left. Multiple that times the impedance of that long wire and you will see there are lots of volts drop. That forces lots of current thru your house, enough to take out lots of equipment.
Since the impedance of a wire at 1 MHz is almost due entirely to its inductance (resistance is insignificantly low by comparison), and you said that the path of the wiring thru the house was also about 100 ft, for a rough assumption you can guess that the amount of current thru your house will be about the same as in that 100 ft ground wire outside.
To meet the single point ground requirement that long wire has to be short enough to drop insignificant voltage so that it doesn't force currents thru your house.
Not having a wire connecting those two grounds and having a separate ground rod for your radio is worse yet. Probably about half the lightning current entering from your antenna or from the power lines will go thru your house.