1)
I usually put weak sensors on a ship-- at least to tell me if its in hostile territory. As for number, I keep anywhere from 3 to 4 surveyors running at any given time, but I'm a turtler. I am surrounded by precursors on three sides presently, so I'm turtling to the point where my military can handle it.
2) Mass drivers centralize production. Then, I have a freighter pick up minerals when X is available and cart them to earth, cycling orders. I don't like loooong deliveries. So as my resource chain extends, I'll have shorter trips to distribution centers supplied by slow, old freighters, and faster freighters making the long distance trips between earth and the distribution centers.
3)
What I've started to do with colonies is begin with orbital terraforming. Its too bulky, and population intensive, to move terraformers to a site. I put 20 terraformers on mars, moved them to alpha centauri, and have since mothballed them (switched off in civilian industrial tab). I made about 80 terraforming ships, and those now fly around and do their thing. I was adjacent to a good mineral rich system, however. I've got more terraformed worlds now than population to put on them or military to keep them happy.
I've found that if you deliver a load of infrastructure to a planet, the civilian fleet will move population there automatically.
Industrially, my colonies are far to small to support earth-style industry. I have purpose built colonies. Mercury is a population farm, and houses ordinance and fighter factories. Necessary minerals are mined there, and suplemented from Earth. Mars is a research world, as is Histia, a planet orbiting alpha centauri. Its neighbor, Penumbra, is a factory world. Factories and maitenence only. Several jumps out, in Anak Zeta, Artemis is being developed with the goal of mirroring earth-- factories and shipyards. The other four colonies are presently Pop farms and will be developed as I see fit. To build a factory world, I start by sending ~150-250 factories from earth, then order 1000 of them to be produced on site; I typically stop and start production on the factories as necessary, but 1000 factories is a pretty good number for reasonable production. Research components, mines, ordinance factories, and refineries are all shipped from manufacturing worlds: I don't want to set up the logistics to move minerals to too many planets.