It looks like they don't use those types of machinery to unload food. The shot showing some kind of grain being loaded was using a chute and not a bucket or excavator. I assume they use a vacuum system to unload food as it is cleaner and faster.
Though, it is wild to think that the grain in your bread was sitting in a cargo hold which previously could have been filled with coal or scrap metal covered in greases, oils, heavy metals, paints, fluids, etc. I hope they really do clean the hell out of them.
Eh, well, Handymax bulk ships (https://en.wikipedia.org/wiki/Handymax) are 200m long with 5 holds, so that's ~40m long holds, ~30m wide, and at a guess 20m deep. Contaminants picked up around the sides are likely below tolerable levels. (Heck, your bakery is probably schlepping around flour on conveyor belts exposed to greases, oils, etc. Ain't none of this stuff sterile.)
Though, it is wild to think that the grain in your bread was sitting in a cargo hold which previously could have been filled with coal or scrap metal covered in greases, oils, heavy metals, paints, fluids, etc. I hope they really do clean the hell out of them.