I don't think it would unbalance gameplay at all.
That is where you are wrong.
So at 1000lbs per bunker, it would take a single pilot to drop 4 of them?
Last I recall that requires heavy level bombers to get 4000lbs or ord per plane. I think they are too easy to strafe, but upping the lbs required would definitely change base take, base pork, and other aspects of gameplay. For gameplay balance and the ability to change the battle along a front or even just at one base (standard for stopping base defenders from bombing your GVs is to kill their ord!)
You may not like it to lose the ord, but it's lose-able for a reason. Just up from another field. If you're upping heavy you don't need to take off 20mi away. You can risk taking off 40mi away. You're still flying hundreds of miles an hour.