The whole idea of a scout on auto is for it to not need to be micromanaged.
As I understood it, the idea was to 'limit' micromanagement. Not remove player skill entirely from the equation.
If the health of your scouts and information-gathering in general is of value to you, then dig in and micro the scouts. If you're tied up in combat, then park the scouts in strategic sectors (meaning, sectors where you genuinely need to be aware of enemy movement) and deal with what needs dealing with.
Building a scout doesn't entitle you to constant, risk-free, up-to-date information. Like most things in this game, you'll get a decent return on autopilot but you'll get a better return if you prioritize and take the time to manage it yourself. And remember, your opponent is working with the same restrictions as you are.
Besides, at the stage of the game you're talking about, it's not like the few extra credits that go towards replacing scouts is going to break the bank.