Shields also should be classified as commercial not military. That way the armour you have lost atleast it has some protection, from an aggressor else these habitats could be destroyed, single laser gun. Also many time i wanted to atleast have some of my commercial vessels have shields instead of armour to suit the rest of my fleet.
The structural shell comes from a discussion about the habitats that went on for some time in another topic. Long story short the habitats were too expensive and not economically viable and during the analysis of the problem Steve concluded that's mostly due to armor. The only reason structural shell exists at all is so that the cost of the habitats can be brought down. It's utility for other constructs, like fuel harvesting bases, is just an unintended consequence.
And this is where the protection issue comes in. Civilian designs are not supposed to be defensible by themselves, they are supposed to be protected by naval units. That's why even now you can destroy any commercial design with a single laser, it will just take you a little longer if you armor your designs. In addition, as mentioned by 83athom, it's difficult for me to see any real shield as a commercial design, much the same way it's difficult for me to see how you could have commercial ECM. Heck, I'm even against CIWS being commercial components, despite them having no offensive power whatsoever. And to be honest it's difficult for me to imagine any reason to put shields on a commercial vessel other than RP purposes. Fuel harvesters, cargo ships, colony ships, orbital habitats and the like are supposed to be behind the lines and protected by naval forces. Adding armor/shields will only make the enemy waste more time/ammunition destroying them, but will not change their fate if they find themselves targeted (note that as far as I know NPR will always go for military ships first). The only ship that could potentially benefit from shields is a commercial grade fleet tanker you want to keep with your warships to extend their range, but you can just pile armor on it and you'll be fine. Or just make it a military ship with defenses added.
Overall I see very little practical reason to make shields a commercial component and as 83athom pointed out, there's a lot of reasons not to do so as they may the break game balance (such as it is). If you're looking for an example of that, orbital habitats can be built in factories. Why is this important? Because anything that has this component can be build in factories, even if it's a massive terraforming ship with engines, tonnes of armor, weak sensors and CIWSs. Considering the ingenuity of many of the players, I don't even want to know what they would build with civilian grade shields, especially against NPR opponents, whose AI is rather limited.