How I envision this happening: The level of the operation will determine what is needed for protection. If we have capital ships on the field we will want as much defence for them as we can possibly muster to prevent anyone from getting any bright ideas about trying to destroy them or steal them. If we have 40+ people in one area we will have at least some combat ships available to defend them. If what we are doing is of high value (like the bengal) then we bring any and all members into it to deter anyone from even going near the area let alone be able to find out what we are doing to begin with. The exact details of these things I will not put on a open forum because of spies (some people don't care but if we actually end up using these ides everyone will know what we are doing without us even having to leak the information out.)
to respond to your points ill number them the same you did.
1) any time a fleet is moving from one place to another they should be using scouts. If you played EVE then you know this already and I have no doubt in my mind this game will function any differently in that regard. Much the same as you stated here scouting should always be 1 jump ahead and watchful of any possible threats.
2) This is where a scout not only in system but scouts in neighboring systems is a good idea depending on the scale of the fleet you are using in order to give them more time to respond and get to safety.