Efficient ways to gather trade items for shop quests?

You will find majority of the trade items in chests (the rarer items are generally found in the chests in the Followers of Romulus lairs).

The only source of "renewable" items, is the thieves/bandits that rarely attack you. Each one killed will yield a large amount of money, and one trade resource (mostly ones that you'll just sell, but sometimes quest items).

You get quite a variety of items by sending your brotherhood of assassins out on missions. It lists what you will receive for each mission completed so it's a very easy way to gather rare items. If your assassins are of a decent level and you have the maximum amount, you should have no problems.