Mafoon

That actually sounds very cool, if the protection costs resource to run, you get notified how much you have stored when invading forces trigger it and how long that will last. If you can get more there you can just keeping topping it up. This could make for some really interesting game play with groups performing sieges to 'starve' out the protection of large bases while the owners try to war with the blockading forces to end the siege or line break vital resource through to hold out longer. 
 
If it worked this way it should be prevented from just switching it on and off to maximise it's run time. It should have a cool down period proportional to how long it was on. 

I don't think the shielding should be automatically included with every structure it should be a costly and bulky additional unit to add to the structure so that small outposts hastily built and not invested in can be raided and destroyed by small pirate gangs in the normal areas. Purchase a small unit and only the core of the structure where you mount the defences and hide the storage get protection  while if you invest in a larger unit you might be able to protect the entire installation. 
Once your protection drops and you do manage to defend it till they come back up, rebuilding isn't a massive hassle since the blue print for the entire structure is saved you just click repair and it will rebuild if you have the materials to hand. 
This system is also great for mercenary groups, you can put out a request for mercs to come and defend your property, book them to come and sit on it for the duration of the protection drop.
How long the protection stays off shouldn't be too long, longer than 2 hours may be  bit too long for players without a large amount of time and may strong arm people into just sitting at home base for their entire play time. Space guard simulator isn't fun. 

Those are energy pipes, I'm sure there's going to be more, for different uses, like mining.

Welcome to the forums Mafoon!
 
I would definitely favor having conveyor systems throughout ships for the reasons you mentioned. Just adds a new level of functionality to ship building and thankfully that is what is planned.
 
 
I know that you can resize voxels dynamically so you would probably be using larger hull blocks for a capital ship, although you can still use small ones for detail. 
 
I've seen that there will be large scale industrial elements for constructing blueprints but after just looking around for info I can't seem to find anything. I just hope to see appropriately large shipyards for building large ships.