You've touched on a really important point with this topic, and it is an area where drop ship sellers can find problems with transactions.
Buyer orders, pays for it, then refuses to pay extra custom fees when they get hit on arrival, and then the transaction goes per shaped!
I'm not ware of a supplier where you can pay for the different duties into different countries up front, apart from that I would suggest that where an import duty is applicable on a sale, that would destroy any margin you originally had on the product anyway with drop shipping.
If you are listing on eBay, you need to make sure that the location you enter is the location of the product, not your actual location if there is a difference. This should be enough of an indicator to buyers to know if there will be importing issues for them when considering purchasing.
Of course it's also an eBay violation to provide a misrepresentation of an items location.
You could also make buyers aware that certain import duties may be applicable when purchasing in your items description, if you are offering international sales, but most people understand their own countries import regulations and will be able to tell from the item location if there will be a problem for them.
Btw, New Zealand has some sort of an import duty buffer, not sure of the actual amount at the moment, but you shouldn't have any customs drama drop shipping your average low cost products into NZ
It sounds to me like your biggest issues will be shipping price and delivery time, I would suggest they are the two areas you would want to focus on streamlining.
Quit a few Kiwi members onboard here, so I'm sure some of those would be happy to share so advice with you on the subject, nothing speaks louder than experience : )