Well remember eletromagnetic disruption only affects eletronics, not actual matter (Otherwise IRL EMPs would be the most powerful weapon ever) The only time you could disrupt matter with an EMP is if it was on par with the output of a magnetostar, which has fields so powerful it strips atoms, but you would need insane (and I really do mean insane) power generation and field emitters for that, but then it would rip apart whatevers creating it too XD
And well also remember the Higgs Boson is a particle which was generated in the big bang that gives other particles their mass, but the Higgs is such a large particule it decays so fast you need LHC level sensors to detect it, because it decays into smaller particles such as quarks, it dosent have any effect on the universe when creating another one, and 'taking it away' would mean decaying it which is what it does anyway which again dosent affect anything. If your looking for something that can destroy a universe somehow in the manner you describe, I would recomend looking up Quantum vaccuum collapse
Even though dark matter can seemingly bind things together it cannot stop anything, it cannot stop eletromagnetism or energy and it cannot stop physical matter either, the only effects it has are gravitational wise, and even then so minute that you have to have entire sections of the universe saturated in it for it to cause galactic clusters, which are just clumps of galaxies