Cannons in bases (and I guess vehicles) are statted up as multipowers with regular Ranged Killing Attack against walls and similar targets; line AoE, No Range, Ranged Killing Attack if shooting forward (For people unfamiliar with HERO, No Range means that the target point has to be adjacent to the user, so the line area of effect would effectively start at the cannon and extend from there); and Explosive AoE Ranged Killing Attack for modelling all types of shots that are explosive/shrapnel etc.
Bases and vehicles are the same rules with a base just being a vehicle that doesn't move so that part yes, will be the same whether the canon is in a fort or on a ship. As to the rest, I think the best question is what do you
want them to be? Is it going to be a common occurrence for cannon to be shooting people rather than ships? How much weight to your decision do you want cannon firing at people to be? I found Hero 6e to work well for both realistic and semi-realistic normal scale people and combat.
That said, anyway:
The issue isn't that AoE is onerous, the issue is that specifically Explosive AoE is onerous. The Explosive modifier on AoE makes the attack only have full power at the point of impact and then it loses 1 Damage Class for every 2m of distance from there. So a 4d6 RKA would do 4d6 at the point of impact, 4d6-1 2m away, 3d6+1d3 4m away, 3d6 6m away and so on. That's just way too tedious to calculate. It's simpler when calculating normal, not killing damage, but it still takes too much time.
You're overcomplicating this and I think you may also have dropped a partial DC in there based on the +1d3. Here's how I would do it and how the book recommends:
I'll do a normal blast first for explanatory purposes. Someone hurls a small keg of gunpowder onto the ship's deck at the feet of some hapless sailor. Lets say it does 6d6 base damage.
I roll to hit. I succeed and the explosive lands exactly where I want. It does 6d6 Normal Damage. I roll and get: 1, 3, 4, 5, 5 and 6. The hapless sailor at ground zero is going to take all of that which is 24 STUN damage and 6 BODY damage. (For everyone reading along, you just add up the results to get Stun and you count the dice for body damage, with 6's counting double and 1's not counting).
There are a couple of sailors standing 3m away and another standing 5m away. According to the Explosion rules, you remove the highest dice first, reducing by 1 for every 2m. So the two soldiers at 3m away take 1, 3, 4, 5 and 5. No re-rolling. And the maths is easy - you just deduct the result of the removed die. The both take 18 STUN and 4 BODY. And the soldier at 5m away takes 1, 3, 4 and 5. So that's 13 STUN and 3 BODY.
It's two dice rolls no matter how many people you hit. Yeah, you technically have to add the numbers up for each range zone with people in it but if the first result was 20 and I've just removed a 4, then that's 16. All in all, pretty quick.
Now if you're the argumentative sort you might be reaching for your keyboard about to tell me your example used Killing Damage. I just wanted to use the simplest example as we're not the only two reading this thread. But to convert this to Killing damage is only a minor change. The explosive rules in the book just say to choose one of two approaches. To reduce it by one die per 6m instead of 2m. Or to just full on remove a static 2 points of damage per 2m.
Honestly, killing damage is actually less maths to do than normal damage.
Hope that helps.