Make reloading automatic. When that is done, the reload simply becomes a delay at a certain point during combat, scaring the crap out of the player. Not now! Of course, it also serves as a reminder of how much ammunition they have left. You can be sure that a player who is waiting for that multi-second reload process to complete is checking how many reloads he has remaining.
Manual reloads could be possible for those times when there are just a few rounds left in a magazine and the player would like to cycle his weapon(s) into the next magazine to avoid a reload at an inconvenient time. When you do that, and a ship carries many magazines, you then start to think about repacking magazines (to consolidate the rounds in the partial magazines into as few whole magazines as possible).
As for ammo pools, they should match the control options.
If I have one switch to throw to turn my point defenses on and off, then I have one ammo pool. It doesn’t matter how many turrets there are because I think of my point defenses as being either on or off. The HUD would reflect that.
If I have four sets of point defenses (front, left, right, rear), then I have four ammo pools and four HUD indicators. That means that if I’m using tactics that tend to result in enemy ships approaching from my front, then my front point defenses are going to run out of ammunition before the other three sets. I then have to either retire or change tactics.
But anyway, the control system drives all this stuff because that’s the way the players will think about employing their weapons.
Ammo pools could have reloading as well, with an ammo pool divided into “magazines”. So those 20 weapon turrets might be fed with a series of three magazines of 50,000 rounds each. The point defenses go down for a few seconds as the system switches from one magazine to the next. The turrets themselves just become damage emitters for a given weapon system.
As ever, the overall gameplay determines how this stuff really needs to work.