Whether the design choice of input registration by the development team in regards to shielding was good or bad should be irrelevant to this discussion. The game is what it is, and if you support allowing the removal of springs, you support non-default controllers. It's very simple.
In most fighting games, the rules for controllers are that they can be just about anything as long as it doesn't allow you to do something that would otherwise be impossible or somehow assist you directly in input. The line here is usually drawn at any sort of a macro that allows one button input to count for inputs on multiple frames. That is, if I want to use a button that presses down + B or A + X on the exact same frame when I hit it, that's fair game. If I want a button that presses Z every frame or inputs a perfect macro to do an optimum DACUS, that's not okay. In terms of how you physically make the buttons, the former cases are all just double wiring two things to the same output into the console. The latter cases are basically putting a chip in the controller and programming it. Of course, I don't know exactly how the GC controller is made; any custom controllers would have to only be able to accept exactly one analogue stick input press at a time (so holding right on the actual stick and pressing the down + B button has to have either the right or the down take priority and not consider both at once), and for the sake of true accuracy, LR and UD inputs from the dpad shouldn't be allowed either (though I can't imagine how they'd be helpful).
I think the other fighting game position on controllers is generally more sensible than what smash tournaments usually do, but if you support what smash tournaments usually do, allowing exactly one gameplay relevant modification (spring removal) while not allowing extra non-macro buttons or anything like that just strikes me as inconsistent. Time has mostly shown the option to have these sort of things is irrelevant since it at best barely improves performance (it's small enough that even at a high level, it really does not matter), and the cost of making such custom controllers is prohibitive for most people.
Do consider the fuzzy other cases as well. I know a local smasher who replaced his left stick with a second c-stick because he likes how it feels better. I've known of other people replacing the c-stick with a second left stick, and I've known of people who import sticks from Wii Remote Nunchucks because they are more responsive than GC sticks. You could have a sticky button on your controller; would installing a replacement button, potentially one of higher quality than the original one the controller came with, be against the rules?
You also have a small number of people wanting to use converters to play with non-Gamecube controllers which I find very hard to justify banning. I remember one guy on the forums a while back wanted to play with a N64 controller; why, honestly, should he be disallowed from that? I can really see why someone might want to use an Xbox360 controller, and there are always the group of crazy people who think PS2 controllers are something other than the biggest pieces of garbage we collectively have ever used as input devices for gaming.
In summary, the rules are restrictive usually, but they really shouldn't be.
