Hmmm...
Maybe torpedoes should have more mass. They're supposed to be massive modules of destruction. A buff to their kinetic damage and increase in their velocity would also help balance out their mass.
If a small ship decides to stack up on torpedoes then the cost in mass should be represented as compared to the ship's mass, so the ship's max speed is much less and their shields less effective. For this trade-off torpedoes should do more kinetic damage and travel at a faster speed. 300km/s should be good, no?
No. Even at 300 m/s they can be still outrun but almost any ship engineered and boosting. The weight would primarily affect couriers and vipers, and these are not the most common torp runners (Mambas, Clippers, even DBX better suited for this IMO). For other ships without EPT, the mass penalty would be a minor annoyance, but not significantly alter their ability to land the torps.
Also, your claim 4 torpedos can destroy any shield is wrong. Many engineered 7/8 sized shields can have integrity well over 200 and require 5 or even 6 torpedos, which is literally more than many small ships can carry at all.
Secondly, there is already an fairly straightforward counter to torpedoes which is to not get hit with them. If you're checking loadouts in supercruise as you should be, you should know when they are coming and evade appropriately.
You seem to make to want it harder to defeat massive shield tanks with absurdly strong shields when they are already overpowered. Do you just feel small ships should literally have no way of taking down larger ones? If so I disagree, and if we take away shield counters (reverb torp/mine, cascade rails) then basically every battle is just number stacking a vette/conda/cutter and facetanking each other for an absurdly long amount of time.
If your problem is not inherently about smaller vs larger ship PvP, but instead getting ganked in a large warship... well that's just not an issue IMO. A well built cutter/vette/conda is nearly ungankable if flown and engineered correctly (in fact most ships are ungankable flown and built correctly but especially something with at least 10k hit points).