I like to think that they interact with whatever force allows Pokémon to manipulate matter and whatever. In some way, apricorns resonate with that energy and allow it to be captured, pulling the Pokémon in with it. Modern balls just emulate this resonance and make it a little more precise. The Master Ball, for instance, has a reactive mechanism on it (the two purple bulbs) that makes the Pokéball always resonate perfectly with whatever its trying to catch. Specialty balls like the Net and Dive perform a similar function by being tuned to the energies normally associated with Bug and Water types, respectively. Shit like that.
It's a loose headcanon, but it's the only pseudoscience-y explanation I've conjured up that accounts for apricorns.
