It is possible to destroy them. It's just hard.
I had been curious about this as well and when I hit level 26, I loaded my ship up with a bunch of upgrades and went back to that starting mission, Balosar Outpost. You CAN blow up that shielded antenna on the bottom, and you don't need protons to do it.
When doing the mission, I saved a lot of my missiles for the antenna, and I launched missiles at it and fired at it whenever possible. On one of my last passes at it (probably put about 20 missiles in it, plus a lot of gunfire) it blew up and I briefly saw a bonus objective message appear in green text across the screen for destroying the antenna relay. Note that it was an "unadvertised" bonus, as I hadn't seen it in the quest log.
I was also able to do this on the Makem Te Assault against the shielded node on the destroyer, too. My ship is fully upgraded (for level 27) and it took about 30 missiles plus a lot of concentrated fire, along with the augment thing that has guns do more damage while shields regen slower. When it blew up, again I got a "hidden" bonus objective complete message.