The ideal "barnacle" design would be to make the exposed surface of the pod just as heavily armored as the rest of the outer hull (the pods extend pretty far into the ship after all, so space isn't an issue). This would give you advantages in defense...aspect to incoming enemy fire...and planetary atmospheric reentry. Obviously, you'd need an ablative system for the rest of the hull, but that's to be expected. Personally, I like your blow-out panel system better, because the pods would then be uniformly armored to their scale. I'm using a similar system for saucer warp engine field grills.
Been following this since the beginning, Vektor. I give it four thumbs way, way up.
"All life is struggle, from first breath to last."