Shuckle is not anti-meta. If your opponent is setting up rocks on Shuckle and not expecting Encore, your opponent is not good. The only set currently listed on
Shuckle's strategy page is the Utility set. If I encounter a Shuckle, on my current team I might switch to Musharna on the toxic. You'll be poisoned due to Synchronize, and then I'll use Heal Bell. Or maybe I'll switch to Roselia, which you will be able to do absolutely nothing against other than Encore my spikes, which guarantees me two layers right off the bat. Or maybe I'll switch to Gurdurr, get boosted by toxic, and Drain Punch you until you die. Or switch to
any other member of my team, absorb the toxic, KO you, then use Heal Bell (and for the record, most good NU teams will have a cleric due to so many great Pokémon in the tier filling that role (Musharna, Lickilicky, Misdreavus, Miltank, Roselia, etc.).
If your opponent uses Trick or Switcheroo, Shuckle becomes useless.
If your opponent uses Taunt, Shuckle becomes useless.
If your opponent uses Substitute on anything other than Encore, Shuckle becomes useless.
If your opponent switches in a Poison- or Steel-type, Shuckle becomes useless.
Shuckle is not good. It doesn't have a niche. And no, it's really not that hard to kill.