This person I am playing with says Ion cannons bypass shields when you take a damage and goes straight to hull, I am 99 percent sure this isn't the case but could I get some confirmation.

With a ion cannon, the defender suffers one damage.

Rulebook page 16 suffering damage tells you what to do. Which means shields work.

Edit:

Stuff which ignores shields deals a damage card.

You are correct. Damage is damage and us all handled the same, remove shields then deal cards.

The only way to bypass shields is if something (like proton bombs) doesn't say to cause damage, but rather to deal a damage CARD directly. Because the effect is skipping straight to dealing cards shields don't effect it.

You are correct. The only way to bypass shields is to deal a damage card, not deal damage.