I would imagine there are either inerting protocols in place or provisions for venting in all antimatter situations.
An antimatter interting system would dump the antimatter against a really dense really heavy piece of something and let it 'burn itself out' in a controlled way, dumping the resulting particle bath and gamma-rays through a wave-guide. Such a system would be useful for small amounts. Larger tanks would have a venting system in place or an outright jettison system.
Neutronium laminate? I'd hate to be the bastard who has to glue that in place.
They used a 3D printer. It's all good
It's an interesting premise to think of the deactivated "antimatter fuel system" in the warp drive pods to have vented out their supply. But what about the antimatter not in the warp drive pods? There is the antimatter fuel in the engineering hull ("That Which Survives") and also possibly the antimatter fuel on Deck 11 in "Errand of Mercy" to consider.
BTW, I do agree that the antimatter fuel is generated as needed instead of giant fuel containers as portrayed in later Trek.