Do the math. The guy shows up with 300 "armed" troops. Attacking them and assuming 1:1 ratio will cost you like 40k losses.
If he has 300 goods, maybe you can sell them for 18-20k to recoup some expenses (and use your S&D anyways in the process).
So net loss to you of 20k to protect your S&D. Maybe an idle clan can afford that kind loss to protect their principles but it becomes a lot dicier for a clan at war to be sending frontline parties to take losses dealing with smugglers.
40K?? First, independent traders have trouble filling rosters, so you only lose a few troops compared to them and you get all their undamaged gear and 50% of their used gear, which right there pays for most of the attack as most guys overspend on gear, while smart clans get more average level gear to equip more troops. The 300 goods are from a ways away most likely so can sell for at least 70 gold upwards of 100 gold in our high price fiefs netting 21-30K. To equip ana rmy of 400 to beat him we might use 40K, but we are not using all that gear or all the troops up and we can reuse that force toa ttack other traders or do other objectives. We will attack everytime - it just makes economic sense - we have come out ahead every time so far.
Plus in a world prepatch (this one) very limited S&D, the prevention of traders trying this and maybe getting away with it saves hundreds of thousands of gold in our own trading, so well worth it.
But like I said, with the recent changes to prosperity, we will likely open a couple border castles for selling at reasonable tax rates in a week or so and so this has all become a moot issue.