I would like a reset-button more. Klick on it and all wares' destiantions in the empire become immediately recalculated. That could melt down one or two jams and alleviate problems in seafaring. Maybe restrict it to be hit not more than once in five minutes or something like that.
If there really is the desire to forbid wares to pass specific flags, I would put them into groups. Let's say there are 4 groups, give them numbers, colors, animal-symbols or whatever. For each flag, each individual group can be enabled or disabled, which is shown on the flag itself. In the target-values' menu the player should assign the wares to the groups (wares can belong to more than one group). Technically this would be the same as giving restrictions on each ware for each flag, but hopefully with a bit less need of calculations and less potential for confusion and so called user-caused-errors.