The majority of lightning strikes are intracloud - a strike between clouds - which is not normally of great interest. Its cloud to ground or ground to cloud lightning that causes the damage. Basically, the electrical charge needs to be dissipated so the shortest, lowest resistance/inductance path will always be chosen.
Without going in to great detail the best protection is to provide that low resistance/inductance path to help the discharge. There is a danger from Rise of Earth Potential (ROEP), from the point of strike the charge dissipates with distance relative to ground resistance which can cause problems if there are multiple earths that are not connected together, that's a common cause of equipment damage and failure.
In the UK our designs for things like signalling equipment rooms are nowhere as good as, say, France. They design their equipment rooms to be Faraday Cages - which is the case for HS1 - whereas the UK uses REB's which don't give the same kind of protection. The rule for lightening protection conductors is as straight and as short as possible - no curly pigs tail like connectors, they form inductors - with an earth resistance - rod or mat - of not greater than 4 ohms, the lower the better. Also, do make sure all metallic items along a route - including fences, return conductors, location cases, structures, et al - are all connected together and earthed at regular intervals.
The probability of a direct lightning strike on either the 25kv catenary or 3rd rail is extremely low, they are not easy paths to earth, more likely to be a structure - signal gantry, OHEL support, lineside structure than a non-earthed item.