This is essentially an engineering question. Dangers, or risks as you'd typically call them in engineering, have two aspects: probability and outcome. Something can be a high risk because of a high probability, or because of a serious outcome.
In the case of anti-matter, any significant containment failure would result in a catastrophic loss, so it's an important risk regardless of probability. The main reason for this is that the amount of energy on even a small containment failure released is very high, which will likely lead to the loss of the whole containment system, and thus the instant release of all energy on-board. And this release will be in a barrage of high-energy radiation, some of which itself will be anti-matter (fast positrons).
That said, you probably can't entire eliminate all leakage. There will be the occasional atom escaping the containment, and violently reacting. You'll need a secondary liner which should survive the duration of the trip; this is very much sacrificial. The main goal is to handle the secondary radiation; it should harm neither the confinement nor the ship itself, all the while being lightweight.
This would be true even if we somehow could manage to store the antimatter outside the actual spacecraft. This isn't easy, but we might be able to keep it confined just outside the ship, in the near vacuum of space. Still, that would be close to the ship, and probably close to half the anti-matter escaping confinement would still hit the hull. But that's OK, the hull was designed for that anyway.