So in ships combat each round consists of 30 minutes of shipboard action in which case what is the purpose of initiative?

Initiative makes sense when two people are fighting in rounds of a few seconds - it then really matters who manages to get their shot off a fraction of a second faster for example.

But if two ships are blazing away at each other for 30 minutes firing hundreds or thousands of macro cannon shells at each other surely initiative is now meaningless?

Both ships should do their damage simultaneously at the end of the strategic turn?

It more realistically portrays the drawn out nature of capital ship battles (back in the old days).

Yes pretty much that. Initiative is just because some sort of turn based system is needed. So it is completly normal, that, say enemy ship blows up, but the enemy already has done something from his next turn. So its just for convenience.

Of course, it can be important. After all, it can be reasonable, that, upon destroying an enemy weapon, it should already have fired. Just apply a little logic to it and judge depending on the situation. So if your gunner started heading to the weapons at the begin of the turn, barely got a shot of in this turn, than that weapon he shot may not be destroyed. If however, he was already waiting, just to get in range, which happened immideatly, than it would be reasnoable, that the enemy didnt get a shot of.