Good grief, another one of these threads. I usually refrain from responding and adding to the chaff, but hey, my 2p...
The thing is, the OP isn't wrong, exactly. There *is* something off about the balance of the game. Not the one-shot thing though - as others have said, you would entirely expect that ships highly optimized for one purpose would fail pretty hard at a totally different one. In our world, nobody's going to build a race car that would survive a tank round, either. Thing is, in our world, you also don't expect to have to put on battle armor to cross the street. There's a general expectation of safety, or at least that the powers that be don't generally tolerate psycho killers on every block.
So one question worth asking is, is that a reasonable expectation for the Elite world? I'm legitimately unclear on this point. It's entirely possible that Frontier intends to make a game set in a dystopian world where governments are unable or unwilling to control the roving bands of mass murderers. Plenty of games are set in worlds like that, after all. It's a bit out of step with the generally upbeat tone we get from Galnet and such, but it's conceivable. On the other hand, if that *isn't* the developers' intent, then something is definitely wrong, but the trouble lies with ineffectual C&P and a lack of engaging content for advanced players, not the engineered weapons.
On a more micro level, it seems to me that the logical balance between exploration ships and warships would lie around stealth or evasion. The PvP folks around here say that if anything, physical defenses need a nerf, not a buff, and I see no reason to doubt that. There's also no reason to expect some long-range DBX designed for the deep black to be able to tank a volley of plasma death, but I would absolutely expect such a ship to be able to avoid the star destroyers. Either through using agility to beat the interdiction, evading in normal space, flying under the radar, or just generally being faster. "Avoid the system where the interesting gameplay is happening" definitely shouldn't be the answer though, because that's just terrible game design.