Partially this is an artifact of the current contrived campaign setting.
It's very Dragon Quest. You fight lots of things weaker than you are, to get money and XP to be able to trounce more powerful stuff.
In an even fight, the hi-tech ships would take hull damage too. In a really close fight, you'll lose a bunch of ships. In these cases, lo-tech wins both by being tougher once the shields are sabotted to death and by being cheaper to replace.
I understand the full campaign won't let the player pick only fleets they can overwhelm. You'll have your own fixed points that can be attacked.
Come to think this is another reason I really like how the fleet point system doesn't let you simply deploy everything. There's a reason to drag around a mix of high tech and low. Hi-tech for when you're attacking and going to win.* Lo-tech for when you're being attacked and you know you're going to take losses.
*(Math: Let's say the hi shields can take 10 000 damage, and lo can take 9000, spread across the deployed ships. If you take less than 9000 damage, it doesn't matter. If you take much more than 10 000 damage, you're in a close fight. Between 9000 and much higher than 10 000, each additional hi-tech ship absorbs a bigger percentage of the damage you'd otherwise have to repair, despite only being a slight difference in overall durability. Going from 9000 to 9100 of 10 000 damage is 10% of the damage. Going from 9500 to 9600 is 20% of the remaining damage. I think the real spread is wider, but the principle of increasing returns holds.)
Also, part of the problem is that, right now, losing even a single ship is often huge and is somewhere between very time consuming and impossible to recover from. The cost is way out of proportion to how suddenly ships can die. If one of my capitals goes down, that's hours of fighting to recover from the elite deaths alone, even if its the only ship that took damage. I stopped using fighters due to their overpower, but if I lose enough Thunder wings, they cannot be replaced at all.