One should get educated about customs duties and the associated surcharge and cess applicable. No matter who the carrier is, these are applicable. These charges are rules and anything lesser is an exception and should be attributed to good luck. Factor in the worst-case scenario and hope for the best.
I've imported and still continue to import various articles for my business, or otherwise. From my experience, knowing the rules is good for knowledge purposes only, you can't challenge the department, especially when it comes to customs. At the end of the day it is the prerogative of the customs officer to value the goods and charge duty on it as he sees fit, he is within his rights to do so.
And there is no provision to challenge this,
(Read: not worth it) you either pay the duty or reject the goods.
Since the past three years, the officers have become extra strict, mainly because of the influx of goods imported from China being heavily undervalued or marked as gifts. This is one of the reasons articles marked 'Gifts' are also taxed now. Rules say that you can import articles of Rs.5000 or below, marked as gifts without attracting duties. But the authorities have become suspicious of importers misusing this exception.
I do not understand how using EMS as a shipping provider can take out the Duty component.
The general understanding is that nobody imports articles of high value through EMS. Most of the time the goods sent via EMS pass through the department without a hitch. In the rare case that you're taxed then it'll be as per the tax rules. No extras charges. This has been my experience.
Eyes of the officers light up when they see packages from FedEx and DHL, as they know that you've paid these services through your nose to ship something expensive, or of value.
I prefer the EMS route for all my imports, if available, not had a single unpleasant incident in 10 years. The only issue is the time it takes. The fastest I've received an article is three weeks, the slowest has been three months.
If your package is held up at the customs when you send via EMS don't even bother calling them. They'll see that it isn't something of great value and eventually send it across to your local post office, with duties to be paid, if any. They HAVE to send the goods to your post office, they cannot withhold the goods, unless the goods are illegal. The most my parcels have been withheld is 45 days.
Rejection of paying duties or refusing the parcel can only be done when the postman brings it to you, not before that, assuming you haven't contacted the Customs Dept.
Hence my suggestion is to never get in touch with them. They'll harass you and charge you exorbitant duties if you do!
Hope this helps. Cheers!