hey, you've got a few things wrong
fist off, whenever you colonize a new planet there will always be, at least, one colony ship being used (for the initial colony planetary improvement). that ship is simply deconstructed and its material used to establish the new colony.
the same mechanism applies whenever you invade a planet with soldiers, although if you lost a lot of your invasive force then more troopships are lost. as a rule the remaining soldiers do still have to have a place on a ship.
there are penalties to shot-down freighters:
- the mini-freighters restart at their spawnsite which naturally yields the lowest income. the more a freighter moves towards its destinated planet the more is your income.
- if a specific freighter is shot down multiple times then the route will be cancelled
if you want to establish a traderoute very fast or early you could trade for enemy scouts and upgrade them into freighters. you'll need some miniaturization & sufficient range for that, tough.
mini-freighters don't cash in on the speed of the original ship. they always move at speed 1. but they can profit from other stats. you could arm them but mostly they won't be able to withstand much pressure, and this is going to cost you maintenance. a good idea would be to place a lot of sensor mods on them so you can peak around into other terrain while the freighter moves. 
