The fact that a facility can be completely destroyed by bombers will encourage strategic bombardement if the price of new purchase is significantly higher than the price of repairing. IMO in OOB the risk to lose a bomber to AA-fire is not worth if the owner of the facility perhaps has to pay 1-2 IPC (maximum of 4 IPC) to activate it again. I would only bomb an air base or harbour under some rare strategic circumstances. Factories are another question.
Therefore and because of there capability to produce I would set the cost to
- air base 12 IPC (we use that price already in our house rules, of course without producing capability, so perhaps only usage for me)
- naval base 15 IPC
I would keep the built in AA in that case.
The possibilty to produce in naval and air bases , especially on islands, may have a high impact to the balance of the game:
US 1 may produce up to 3 fighters and 1 DD or 2 fighters, 1DD, 2 sub (max 40 IPC) in Philippines. - A J2-attack will need some more units.
US can produce in Hawaii, Midway, Guam (so perhaps NB in Midway or Guam should be removed from setup)
From round 1 on UK can produce ships in Egypt or Gibraltar.
Japan in Carolines (AB and NB)
Java could become an interesting hot spot, especially for US.
One more detail: An AB or NB has to be completely repaired (no more damage) if you want to produce 3 air or ships there.
I like the ideas that factories a maximum damaged (AB and NB 5 more damage) when conquered, that you steal 10 IPC and the owner of a former capital can go on producing (so France is more interesting).