You’ll need to use motion controls to catch Pokémon in Pokémon: Let’s Go Pikachu and Let’s Go Eevee, regardless of whether or not your Switch is docked, and they’re compulsory throughout.
There was a suggestion this was the case from the off but, in a statement passed to Eurogamer, we received the following confirmation – and clarification – of how exactly the new catching system works:
“In handheld mode with both Joy-Con attached – you are still required to move around to aim, but you press a button to throw the Pokéball.
Source: Eurogamer Motion controls are compulsory for catching Pokémon in Let's Go Pikachu and Eevee