Yes it will.  I often pick and chose the optimal route, and only build tradeports ont he route, or in a position that will not shorten the route.  You can easily get double or triple income from your trade port with careful planning.

it really depends on how much longer you're going to be making the route by removing a badly placed port. it also depends on how many trade ports you've already got built and how many your planning to build.

for example, you might gain .2 creds/sec on each port if you lengthen your route by 1 jump. if your existing routes produced 1.6 creds/sec per port then you'd have to be improving at least 8 ports (existing and yet to built included) before this could be considered a net gain.

moral of the story is try to plan the route before you build too much so you don't end up in situations where you have to scuttle trade ports to re-optimize the route. 

The reality of the game isn't quite like that, since planet bonuses (ie: +30% trade revenue) may be enough to convince you to shorten your longest trade route, and in reality you are unlikely to fill every viable logistics slot before the game ends.  As well, the longest chain disperity between trade spam and a planned build tends to only become significant after you control more than half the galaxy.  This is particularly true on those huge sprawling single-star systems.

In the above example linked by SageWon, if you controlled only the top or bottom half of that system, the difference between spammed ports and a planned route would be 1-2 jumps, depending on how you count.  This isn't a big deal.  The issue of trade disperity only rears its head once you start to pick up enemy territory, at which point it may well be a moot point anyways.  I find the longest trade route analysis comes into play most often in huge multi-star scenarios, where you do control entire solar systems and can plan them out.