Note that for low-volume production, contracts manufacturers will normally be able to deal with all non-standard components from their own stock. It will only be components they are not interested in keeping partial wheels for that you will have to pay extra for. And if the contracts manufacturer has designers to help customers with new products, these designers will know which components the factory stocks, and which components that will have to be bought specially for this product.

Some contracts manufactuers can also supply a list of their stock components, if you intend to use an external consultant for the design.

The next thing is that the price difference between hole mounted components and SMD components can be so high, that it is cheaper to use SMD components and throw away or sell on the surplus market a very significant part of the wheels.

In the end, the biggest issue is normally not the selection between SMD or hole-mounted components, but to select the most common components.