If I read it correctly and understood it, a Runabout (which still counts as a shuttle, and without my modifications or your suggestion above) with or without the attack pod could pose a threat to scale 3 craft at the very least, possibly even scale 4. If they hit, and roll the 4 CD for damage, then spend momentum either on re-rolling part of the damage, adding directly to the damage, or removing resistance… One attack could easily cause a breach. With a really good (or lucky) roll they may not even have to use momentum in order to acquire that result.
I am not purposely trying to be contrary or argumentative, I am merely point something out that I believe is a possibility. Just because they are small craft does not mean they are not a possible threat. Two or three Type 6 armed shuttlecraft could pose a problem to a Klingon Bird of Prey. Being small craft, the difficulty to him them is increased according to the rules. Might not be enough to outright destroy the BoP, but they could possibly disable a system or two if played strategically, like within an asteroid belt that would provide cover for the smaller craft but not the larger one.
If I am completely wrong and off base, by all means correct me. Granted, if played out the BoP would probably disable the shuttles before it could be disabled, but there is still a chance that the shuttles could be victorious. (Most likely not undamaged, but still victorious.)