The idea of having a long chain of planets with trade ports is that for each planet in the chain, the money earned from trade ports increases. However, I've noticed the algorithm for finding the "longest" route functions in an odd way: it finds all the shortest routes between your planets and chooses the longest of those shortest routes. In effect, conquering planets and building new trade ports could potentially lower your overall trade port income. For instance, if you owned five planets (connected in a line) on the rim of a solar system and they all had trade ports, your longest chain would be five. If, however, you conquered a sixth planet which connected the first, third, and fifth planets, and built a trade port there, your longest chain would be three: from planet 1 to planet 6 to planet 4. The chain of 1-2-3-4-5 is no longer applicable because the route between planet 1 and planet 5, after conquering the sixth planet, is shorter by taking the 1-6-5 route.

I don't recall the actual income boosts for trade ports. However, assuming it starts at 1.1 per planet and increases by .1 per additional chain, the first five planets in the above example would give (1.6 x 5) = 8 income. After obtaining the sixth planet and building a trade port, the income becomes (1.4 x 6) = 8.4 income. One thought I have is that this is to balance the game, since in this example you are still gaining more income by building the trade port at the sixth planet, but not as much as you'd expect (so as not to exploit large trade port chains). However, in situations where you have a very long chain, and conquering a new planet greatly shortens that chain (especially if it is one which has gas planets and other uncolonizables adjacent to it), building a new trade port actually decreases your trade port income.

Was this intentional, or does the "longest-chain" algorithm not function as originally intended? In any case, it's something to think about when you next think about where to place your trade ports.