No you do not!
Naturally, we understand that there may be some items that a merchant would only want to sell online or only in their brick and mortar store. These items do NOT have to be linked to the opposite platform at all.
You should also not link products that you do not intend to track inventory on. If you offer custom furniture, for example, on your website that have to be custom ordered or made, you would not want to track inventory on those items on your website as the moment one is sold, it would go to 0 on your eCommerce and POS. In order to prevent that, make sure that inventory tracking is turned off for that product on your eCommerce website and DO NOT form a linking relationship for it between your eCommerce and Point of Sale. (This also works for non-quantity products!)
In order to prevent this a syncing relationship from occurring in these products, either do not push that item to the opposite platform or delete the item from SKU IQ. Deleting the item from SKU IQ will break the syncing relationship. If you have auto-pushing enabled, you can also delete the item from the platform you do not want it on - this will not delete the item from the platform you do want to sell it on! Remember, SKU IQ will not delete items for you unless you tell it to!