I have a store where I complement it with items from the handyorbs plugin, but that plugin bugs when it stacks and I can't find a way to make the store not stack specific objects.

I don't think there is a solution to that. This plugin is supposed to behave like vanilla villager trading and will therefore always create exact copies of the sold items. So any unique ids or other information inside the items that are supposed to be unique are not accounted for. So the resulting items will therefore be able to stack.

There is also no plugin-independent way to figure out whether some item contains information that is supposed to be unique, so that the Shopkeepers plugin could at least ignore such items / prevent the creation of trades for them. I will certainly not add any kinds of plugin-specific integrations. But one idea could be to allow admins to configure inside the config of the Shopkeepers plugin filters / item patterns that would define a blacklist of items for which no trades can be created. I will keep this ticket open for the purpose of this 'feature request'.

However, if you want such unique items to be sellable, one solution could be to sell the item without the unique data, or with some placeholder, and then have the other plugin that is responsible for these items detect and convert the bought items into unique variants. But this would be something for this other plugin to consider, and is not something I consider to be part of the Shopkeepers plugin itself.