The only thing I can find on it is in the
FAQ:
Q: Do units hit by lightning as a result of Imotekh’s Lord of the Storm
special rule benefit from the Stealth or Shrouded special rules due to
Night Fighting? (p55).
A: No.
Now, if Immo's lightning just ignored cover, I'm sure that they would flat-out say that it ignores cover. So if we're not using Immo as a reference point for stealth/shrouded, and the lightning always strikes the side armour of vehicles,
HIWPI would work out cover saves in the same way as a Barrage weapon (only without a blast template obv.), so area terrain (without discussing the RL implications of standing next to a tree during a lightning storm...) or special cover rules (Eldar Warlocks with
Conceal for example) would still work.
Saying that they don't count as shooting attacks is a bit vague. We are only given two ways of resolving hits/wounds in the rule book, shooting or assault, there is no category for "special rules wounds" so unless it states it counts as a shooting attack or counts as wounds caused in combat we're left to our own devices / guesswork.