Customers expect the costs of insuance, utilities, etc, in their cakes. They do not expect to pay for a set of pans for you to keep and reuse.
The cost of supplies, including pans, should be allocated as overhead across all orders taken during the useful life of the supplies. This means that every customer is paying for a portion of all your pans, even pans that aren't being used for their order. Not trying to beat a dead horse here, but I think this is an important point that is too often overlooked when costing products.
If you don't feel comfortable charging back the entire cost of a specialty pan you can charge a percentage you deem appropriate or just add it in with the rest of your overhead, but in my mind that's more unfair since other customers will be subsidizing the customer who chooses a design with a specialty pan.
Many bakers already charge a premium price for petal shapes because of the added labor.
The whole point of a specialty pan or stencil is to reduce or eliminate the added labor, which means the customer saves on labor costs. If the labor cost of the order with a specialty pan is the same as without a specialty pan, there's no point in buying the pan in the first place. By the same token, if the savings in labor is less than the price of the specialty pan, it might make more sense to execute the design without the specialty pan (assuming there is no loss of quality).
Aaaand hope they won't notice.
On the contrary...if the customer asks about the price difference for different designs, I explain that the more expensive design is more complex and will require additional labor and/or specialty equipment (depending on the design). There's absolutely nothing wrong with telling the customer this up-front either.