That is a common modeling issue (also e.g. for pallets that are reused and where maybe 5% do not survive one reuse cycle, i.e. they are returned 20 times), and it can be modeled as follows: Suppose you need 1 pallet for transporting 1 unit of product to the client, the pallet is going to be returned and is reused. Instead of 1 pallet for each product, you only consider 0.05 new pallets, and you model "somewhere" in your life cycle wood waste (or so) with the appropriate amount as output, probably then converted to mass.
LCA is a somewhat simple modeling approach and does not consider stocks, so you do not need to "see" in your model the real number of pallets (or tools, in your case).
However, for determining the transportation weight, you must consider the entire pallet. You can model this as a loop from the pallet return from the client.