RB,

What are the dimensions of the air bubbles? Are they on the inside of the hull at the seam between panels? If so, my opinion is that if they are smaller than 1/4" in diameter, you can leave them. If they are larger than this, you should at least drill a small hole in each end of the bubble and inject epoxy. The risk in leaving them is that water will enter, be trapped, and cause rot or delamination.

Jon