There are two factors that can prevent a ship from being destroyed. Mass of the ship and the experience level of the crew. Crews can gain experience from traveling through space and through combat with enemy starships. Alchemy ships gain experience by using the onboard alchemy machinery. Crew experience is also gained from flying through a storm.
Solid matter acts as a damper against the effects of voltage fluxes.
If you must travel through a ion storm, be sure to load the ship with as much fuel and cargo as possible. Class 4 and class 5 ion storms will drag starships along with them. There have been reports of ion storms with voltages over 451 meV having an unexplained effect on starships. Starships that have entered storms of that power and have ether been destroyed or just vanished, never to be seen again.