Star Trek has significantly influenced culture over the decades. The original show spawned multiple other series and movies. The original series actually featured the first multi-racial kiss on television. Science, engineering, and interest in space in society were influenced by Star Trek. Let alone the phrase “Beam me up, Scotty.”
Snapping Magnussen's neck would be very un-Sherlock. It's a particularly intimate and personal way of killing someone, versus shooting them from a distance away. If the idea is that Sherlock is violating his own moral code by killing someone, I doubt he'd go straight to that level of execution tactics.