It'd require one hell of a balance rework, for starters. Health of hardpoints vs hull would have to be a very high ratio (meaning hardpoints are very weak compared to hull) to make targeting hardpoints at all worth it in large battles, given how much firepower is wasted when a hardpoint is destroyed and all shots in transit do nothing. This would require a rework of every single unit in the game, with new rounds of testing being done to balance them against each other all over again.
I don't agree that bombers would want to target hardpoints, quite the opposite - their projectiles take the longest to hit, so the chances of the hardpoint dying while the torps are en route are the highest. In other mods or vanilla, where torps bypass shields, this would make sense, but in ICW there would be little reason for targeting hardpoints over hull with bombers. Play any fleet battle vs SSD as the NR, and you will watch as tons of your bombers' torps do nothing once the shields go down because the hardpoints die before the torps hit (not the majority, but a high enough percentage that I don't know that I'd ever have bombers go for hardpoints over hull). Maybe in smaller battles, but in large ones where concentrated fire is king? Not a chance. There may be situational exceptions, like burning the weapons off one side of an SSD, but for anything smaller than a battlecruiser I don't know that I'd ever target hardpoints over hull with fighters or ships - more of your fire does its job then.
Also, I rather like the notion that ships have to be taken apart piece by piece, rather than just generically targeted. Many ships in the game are pretty big - a Strike Cruiser is 450 meters long, or more than four and a half football fields. While I wouldn't mind the addition of more targeting options, some of which could be instakills (main power generator, targeting the midway point to cut it in half), it makes sense that you don't just shoot any single portion of it a lot until it dies - instead you'd burn through a portion of the ship, which would lose functionality, and then likely be quickly sealed off by bulkheads with power cut off and rerouted.