I love the mechanic where at one point, if you need more power, you need bigger dimensions, bigger ships. But there is nothing that prevents this sort of formation. If I fill the ship with shield dispersers, those flimsy tubes are as durable the rest of my ship (shieldwise).
Suggestion: Possibly do a check for every block (once after you enter flight mode) and if there aren't many blocks adjacent to a block, it should perhaps get affected by only a percentage of ships overall shields.
For example: those flimsy blocks would do a check in 32x32x32 radius (arbitrary) and seeing it will have very little amount of neighboring blocks compared to the rest of the ship, instead of a 100% of shields capacity they will have 1%(arbitrary), giving the enemy a chance to destroy them, but not the rest of the ship.