It's nice of you to still answere this, but you should notice I asked before the most recent patch when the hit markers weren't crosses and didn't have only two sizes.
Also, even though red hitmarkers do imply the component hit is destroyed, they do not mean the component is destroyed. They mean you damage the permahull. The difference? When the component you hit is destroyed but the hullarmor is still up, the hitmarkers stay white.