Heres what I would do... But it depends on the bubble type in my opinion.
1. Big bubbles that protrude from the acutal mold, I would hit with a knife, dremel, or grinder and rebuild the area.
2. Big bubbles that don't protrude from the mold, i would drill a hole and brush some resin in the to fill the void.
With the larger bubbles I would toss another layer or 2 of glass over the bubbles with 2" over lap if possible.
Smaller bubbles that protrude you can probably leave from a structral point of view and the even smaller bubbles that are in the layers don't even worry about those.
A 1/16" layer of fiberglass can bridge a 1" hole and with hold approximately 80psi. 1/16" layer is roughly 1 layer of 1.5oz chopped strand mat. 2 layer of at roughly 110mils will take 100psi over a 1" hole. So from a structral point of view the bubbles don't truely matter too much. However I don't think you don't want your sub box to flex at all, especially if you are going to paint it.
Hope this helps.