In regular play almost every mon has access to toxic, stealth rock, spikes, toxic spikes, leech seed ect, many other factors to beat Shedninja. In No status pokemon that lack coverage literally can't do anything. Your Mega Metagross is basically useless as Mega Metagross only has one viable move to hit it with, pursuit. Your Altaria might be useless, Thundurus, Azumarill, Breloom, Celebi, Mega Gardevoir, Mega Swampert, Politoed, Kingdra, it all depends on the moveset. As long as you know your opponent can't hit you, your playstyles will be revolving around eliminating those that can, so you either have your whole team running dark/ghost/fire/rock move, centralising, or your opponent will be able to pick your team apart and eliminate the pokemon that can deal super effective damage. Basically any mon can be useless if its not running said super effective move, which centralises the metagame around them.
Well, the only Pokemon that that would really affect are those that have 4MSS with 4 attacking moves (with one of the guaranteed slots not being a type Shedinja is weak against). Mega Metagross always had that problem since there are SO many Pokemon it can take down with different moves
Mega Altaria doesn't have that problem at all. In standard I've seen it run Return and Earthquake often. And then it usually runs Fire Blast for the third move. So it would be stupid to not run it.
Thundurus's "good" coverage includes Thunderbolt/Volt Switch, Dark Pulse, Focus Blast, Psychic, Sludge Bomb/Wave (depends if you want to spread poison well or not), Flash Cannon, and Hidden Power. It's easy to just choose to run Dark Pulse on it if you really hate it (since you can't run status moves on it)
Azumarill's common sets run Knock Off anyways so it's not a big deal for it to deal with Shedinja.
Breloom is crap here anyways since it lost its main niche with Spore so I don't even want to talk about how to deal with a slow frail Pokemon in what will no doubt be a HO metagame.
Celebi doesn't have many coverage options it can use, so Hidden Power Fire is great on it (it's recommended on its only real offensive set as well)
Mega Gardevoir only has 6 main moves: Hyper Voice, Psyshock, Focus Blast, Thunderbolt, Hidden Power, and Shadow Ball. The first three are used. Shadow Ball is great to take down Shedinja as well as Steel/Psychics and Fire/Psychics so it'll see use.
Mega Swampert will probably see less use since it's slow and its ability is useless without Politoed support, but it's definitely better than Breloom. It's physical movepool includes Waterfall, Earthquake, Ice Punch, Power-Up Punch/Superpower, Rock Slide/Stone Edge. It's kind of a wash if you want Fighting or Rock coverage. EdgeQuake coverage is pretty good in general so it might run that.
Politoed has a problem since it has to run Hidden Power and it would prefer running Hidden Power Grass to take down Gastrodon, Quagsire, and Jellicent. But the latter can also be taken care of by Hidden Power Dark (and hey, all 31 IVs there!). So it depends on who you want to wall you. And to be fair, Gastrodon isn't something you really need to worry about.
Kingdra has a problem too because it likes its moves. So, I'll give you that one.
So, out of the 10 you listed, 1 doesn't have a place in this Meta, 2 have problems (but only one has serious problems), 1 has 4MSS, 1 has a slight moveset change from standard that it probably won't mind too much, 2 have moveset spots open for it, and 3 already have solutions listed under their "good" sets on this site. So, altogether 40% listed have any sort of problems (if we still count Breloom) and that was trying to find good problems here.