I read that wine was known to the Japanese but was by and large imported during the edo period. Did the Christians use this imported wine and risk the increased chance of being found out or did they substitute it with something else?
Not sure about the wine portion of the catholic eucharist, but rice balls were used for the 'bread' component. Strictly speaking, in the Roman Catholic tradition, the physical form of the food is of secondary importance. It is traditionally bread and wine, but the belief (transubstantiation) that the items become the body and blood of Jesus means that the 'earthly' form of the food and drink can be any type that is practical. It is likely that sake was used, but I haven't seen a source on that.