I understand pessimism, but trying to rely on gimmicks and spam and then crying foul is wrong. You should focus on strengthening your fundamentals so you have a foundation to rely on, no matter what the MU.
For this MU, zoning is definitely the most important. Range-wise, Samus has answers to many of MK's approaches with definitive, solid options to rely on... except maybe tornado, where it's very situational.
D-tilt is MK's best shield poke. When you're put in that position, your best answer would be between jumping oos back and rolling, both subpar. It's a scenario Samus tends to lose.
But MK's d-tilt also has little hitstun when it doesn't trip, and at higher percents is not as easy to link into a follow-up. If you have fast enough reactions, at close range you can jab it, at far range you can d-tilt it. And you can also outrange it with your own f-tilt.
F-tilt can be outranged with your own. D-air camping can be countered with homing missiles and patience. He has to land, you can punish most of his fast horizontal momentum shifts with z-air, punish his landings on platforms with aerials, pre-emptively hit him with up+b (if sheik, falco and zss can counter d-air camping, samus definitely can with less risk involved.)
Then there's tornado. Most and I mean nearly all MKs can't tornado perfectly. There are key things to note. If the MK comes at you with the early hitboxes of tornado ast a fast pace, you can DI up, get knocked upward and break tornado with n-air, often leading into anothert follow-up for you. If he retreats early and is in position to lag cancel the tornado, charge up so that retreat doesn't become an option next time. If he retreats but doesn't have room or time to cancel lag, you have dash attack, dash grab, super missile. If he tries to cancel on top of you, up+b covers both sides. It's your responsibility to react, it's a four frame window.
If he nados correctly, it won't come as fast but you also won't be knocked upward if the nado connects. If you react fast enough, you can however full hop back and nair, try to zair the top, utilt, bomb; this is all dependent on the space and time available.
And above all else, if it does come too fast, perfect shield and tilt up.
Perfect shield approaching is overrated. MK's risk reward for getting it right is not as lopsided as Snake for example. You have plenty of mixups, between wearing down his shield with projetiles (this includes charge shots, uncharged, half charged, tempo shift is important), spacing f-tilt (d-tilt and d-smash have special circumstances outside of just punishing for use as zoning), foxtrotting or walking back, dash attack, dash grab.
Play smarter. Homing cancel gimmicks aren't going to work if you abuse them. Z-air camping won't work alone. You need to heavily concentrate on your shield pressure play without exposing yourself (yes, I've practically defined what zoning is... But it needs to be said because I'm a hundred percent certain you guys don't abuse shield habits.)
Just refine your skills as a player before you complain or how else do you plan to improve?
If you ever get to the point where it feels beating MK is possible, then I can discuss more subtle things like how to space and time a d-air against double u-air, how disjointed u-smash can be against d-air, shield poking with the samus FIRE style, spiking MK's typical u-air to tornado recovery from the ledge...
Samus is fun, especially when you pull off cool **** like that and win because of it. But seriously, you've got to first learn that Samus zoning isn't just projectiles and walling.