The OP's point is valid and here is why: Recruit mode vs Vet/Legendary. When you go back and play this mode, you will immedietly notice that the game "feels" better. I think this is because this is simply more of a "Pure" game mode. Yes these distruption modules are still in the game but their effects are lessened and also not needed as much because ships like Tacticals and Corvettes are not nearly as strong in the higher tiers ( due mostly because of stronger modules and OB - "Cough" "Cough" Desperate Measures )
Using other games ( WoT ) as a comparison is not helpful.
My problem has always been that the game seems to evolve into a non-sense bleep-show of Modules that do in many ways suck the fun out of the game. Yes there are ways to counter modules but the basic fact is that these modules STOP something or PREVENT something.
This essentially disconnects you from the product *
In a game like this where getting from point A to B can be slow and difficult I think it is bad idea to then also have more things in the game that make it slower, difficult, and downright throw the controller against the wall frustrating. ( and again to the OP's point, Scrambler for example is still the dumbest thing I have ever seen in a game of this type )
Also, I would like to say that I am not in favor of removing these types of modules. They can and should exist to add flavor - but perhaps at the higher tiers and with OB combinations they become too strong? Or the ships that are most vulnerable to them ( ie: Dreadnoughts ) need a buff or maybe as the OP suggested Warp is Standard on some ships...