This seems more like an issue of big ships beating little ones... however I expect you could be right. There may well be absolutely no load out possible for your ship or any PvP ship that can could compete with the raw power of the Heat Weapon meta.
Not at all - I'm not a bad PvP player by any stretch; before 2.1, I was beating a lot of well-known CMDRs in FDLs, Pythons and FASs. Certainly winning more than losing.
Now, I get beaten by modded Vipers and Cobras. All they need to do is hit me with thermal beams then let loose a couple of volleys of thermal cascade packhounds, and my thrusters are gone. Even with Vera mk II, a low-heat build with B-grade clean-tuned thrusters (for extra integrity), that's all it takes for them to malfunction. At that point, it's game over. Bear in mind that this is a ship with which I can empty my WEP capacitor with pulse + beam while boosting and not go over 65% heat.
DB's obsession with making heat the single most important mechanic in the game has broken it, as far as I'm concerned.
As has been pointed out...thermal shock and thermal conduit are better at doing the jobs of all the other special effects. They cause damage regardless of shield status (so they're better than phasing sequence), they cause module malfunctions which are irreversible non-randomly (so they're better than scramble spectrum), they make thermal vent and thermal conduit irrelevant (because they do damage so quickly that your opponent doesn't have a chance to fire back) etc.
While previous rebalances have forced a change in the meta, they were at least manageable. This is just poor design with a total lack of forethought; I say that as a developer for who's made his fair share of screwups in this regard over the last 20 years. The difference is that I owned up to them and fixed them immediately.
As far as I'm concerned, the only fix for this is to remove the special effects entirely. That's where the problem lies; the rest of Engineers is pretty much perfect after the last patch, as far as I can see. Removing the special effects wholesale - while an admission of a mistake - would remove the need for constant rebalancing passes to placate the community, and thus free up development time to be applied to other things.
Can't see them ever doing that, though.