[Baertram]

You'd need to check the file HarvestCount.lua, especially the function "HC:COuntItems()".
There are multiple lines where only the normal inventory "INVENTORY_BACKPACK" is used to count the items.
There should maybe be a check if the user is using eso+ and got craftbag access (if HasCraftBagAccess() then ... ) and then if the items are transfered into the craftbag "INVENTORY_CRAFT_BAG" automatically (not sure how to check this or if this is always like this, if you got craftbag access? Was there a setting to choose if the items get into inv first and then the craftbag?) and then check the craftbag for new entries like the items check in the inventory is done here.

You could try this (not tested):

function HC.CountItems()
    local b = 0
    local r = 0
    local w = 0
    local c = 0
    local counted = {}
    local itemName = ''
    local invType = INVENTORY_BACKPACK
    if HasCraftBagAccess() then invType = INVENTORY_CRAFT_BAG end
    local slots = PLAYER_INVENTORY.inventories[invType].slots
    for i,slot in pairs(slots) do
        if(type(i) == "number") then
            itemName = GetItemLinkName(invType, i)
            if(not SetContains(counted, itemName)) then
                counted[i] = itemName
                local itemType = GetItemType(invType, i)
                if(itemType == ITEMTYPE_WOODWORKING_RAW_MATERIAL) then
                    w = w + GetItemTotalCount(invType, i)
                elseif(itemType == ITEMTYPE_BLACKSMITHING_RAW_MATERIAL) then
                    b = b + GetItemTotalCount(invType, i)
                elseif(itemType == ITEMTYPE_CLOTHIER_RAW_MATERIAL) then
                    c = c + GetItemTotalCount(invType, i)
                elseif(itemType == ITEMTYPE_REAGENT) then
                    r = r + GetItemTotalCount(invType, i)
                end
            end
        end
    end
    HarvestCounterOre:SetText(string.format("Ore: %d", b))
    HarvestCounterWood:SetText(string.format("Wood: %d", w))
    HarvestCounterCloth:SetText(string.format("Cloth: %d", c))
    HarvestCounterFlowers:SetText(string.format("Flowers: %d", r))
    --   d("Flowers: "..r.." Ore: "..b.." Cloth: "..c.." Wood: "..w) # debug
end

MAybe this will not work as the items will be put into the inventory first and then, afterwards with a slight delay, into the craftbag. The function is executed after loot so not sure if this works, you need to try it.