I don't think it matters at all. Trade module's a trade module, man, and once that route's goin', the little freighter guy just chugs along at one parsec a turn, regardless of what kind of engines you slapped on that bad boy. There's no reason to cancel routes and make new ones to the same place, it just starts the freighter over at your end of the route.

Yet, the old ship design comes back to the shipyard because of the trade route, even after deleting the design. Also, it will show in the shipyard the number of those freighters from the trade route (1 for each trade route using that design). If you try to delete the design then it asks you if you want to decomission them?

Does the velocity of the freighter make any difference? Maybe you can get more money in a shorter amount of time.

The old freighter is a core design, it will always be there, you can build new freighters using other hulls as long as you slap on them the right module for trading, the trading route is an eye candy and the only thing you will see from zooming out is the symboil for freighter, now if you zoom in you will see your new design. I did it in my last game, I created a new constructor, a new freighter and a new colony ship.

I n my last game I created a constructor ship on a huge hull and it had 9 engines!!! also I created a colony with 9 engines.

I think that the trade routes have their own speed, but that is not the important part, once you establish the trade route it tells you how many bc per month it will generate, so speed AFTER the trade route is created is no longer a factor, you are going to get a certain amount of bc/per month.

Don't mean to be rude but I don't think you understood my post? Is it not clear in my original post? I'll try to explain better.
I designed a freighter, this freighter had greater speed than the CORE design, let's call it Freight 2. Then I established a trade route with it. Not long after that I upgraded Freight 2 with faster engines and saved the new design with a different name, let's call it Freight 3 for clarity. Then I deleted the old Freight 2 design.
Now, the Freight 2 design just keeps returning to the shipyard designer and is available to build, yet I deleted that design.
Freight 2 established 1 trade route and the design for that ship keeps returning to the shipyard, if I delete the design again it asks if I want to decomission the old ships (there is 1 trade route using that ship). Looking at the trade route it even shows the old design when I click on the freighter graphic. The Freight 2 design will not go away.
The trade route can't be upgraded to use the Freight 3 design (a faster freighter), it sticks with the old design which I deleted.
I hope that makes a little more sense.