Your trade route only needs to pass through the area of effect. However, I wouldn't get too crazy with building econ star bases just to bump trade.
Firstly, trade routes can, and do change frequently during the course of a game for various reasons. Your trading partner can become your enemy, the planet your route goes to is captured by another civ, or simply more profitable routes turn up. I rarely am trading with the same planets that my first trade routes went to at the beginning of the game.
Second, have you calculated the number of mouse-clicks required to build a fully upgraded starbase? For sure, and for certain, your starbases will become targets during times when you are at war, so you will need to put hefty defenses on them. It takes roughly 10 mouse clicks for each module...from selecting the planet to build a constructor, to opening the build list to confirming your selection, then closing the dialogue, then selecting the planet again when it's done, launching it, then selecting the starbase to be upgraded, to confirming which module you want to install.....
Now considering that a fully upgraded starbase can have something like 61 modules (someone correct me if that number is wrong), that's 600 or more mouse clicks for EACH starbase. It leads one to think someone at Stardock held interest in Logitech
I never understood why they didn't simply handle constructors like a planetary upgrade; you select the spot where you wish to build a starbase, you then select what modules you wish to install, you pay for them (which you do anyway in the current system) and are given a time to completion. Simple and user friendly. For galactic resources, you need only the initial constructor to stake your claim on a resource. After that, the above system would apply.
In my own games, I might have as many as 20 or 30 starbases of all kinds, so that's literally thousands of mouse-clicks. My arm and wrist go numb, to say nothing of the wear-and-tear on my mouse. Building constructor after constructor is THE most annoying feature in the game, for me. It's the reason I stopped building the military version and go only with econ bases. Econs will benefit me every turn regardless of expansion, while military bases are used only in times of war, and usually become left in rear areas as my empire expands, and hence useless. Not worth the effort, IMHO.
Yeah...I really don't care much for the way this feature was designed