You can do a lot more if you equip your 'deep penetration' raider with plague bombs.
Just one hit and the planet will become useless to your enemy within a few turns. Provided he hasn't got a medical bay close at hand. There's my second mention of plague bombs in as many Posts.
The rest of the ideas here are very interesting. Having to represent ALL of the ships carrying trade around would be a nightmare. It's completely impractical. SE is a huge game already and full simulation on the scale we're playing is just not possible. I agree that the problem of protecting your logistics is glossed over in SE IV, but the reason is clear. So, 'convoy' protection situations would have to be clearly defined to certain circumstanes.
Having a system akin to the MOO II system where you buy abstract 'merchant fleets' might be doable. Food is not considered in SE IV, but if the total volume of resources produced by your empire required a certain number of merchant ships per so many thousands of of points of resources you'd have a decent equivalent. When you want to send something like population from one planet to another, you have to 'draft' some of that fleet and it is not available for regular duties. This could result in a temporary loss of resources just like a blockade or destruction of a space port.
With this system it MIGHT be possible to have an abstract 'fleet' of merchant ships become a real fleet of transports that your ships have to protect in certain situations. Maybe when ships attack a planet containing a space port? If there were 'merchant ships' carrying resources -- that might be lost! -- present whenever a planetary space port was attacked it would add some importance to space port planets.