Setting <InShop>false</InShop> for items normally found in shops, results in that item being removed from shops AND creative inventory (e.g. /creative_mode or shipyard "Edit Design").
The expectation is that items would remain available in creative/shipyard inventories.
The underlying goal behind reming various items from inventory is to strengthen a player-run economy; reducing NPC dependency. An alterantive solution, could be adding a function that enables administrators to limit the maximum quantity of an item in all NPC shops.