There are timers at all of your factories telling you when a given item will be done being built or technology is done being researched. In terms of queing you can que up to 5 technologies at once and given that the shortest technology training time is 0.5 days that means you can que up several days worth of research in a single go. If nothing is left in the que it will begin researching the next rank of the last technology that was researched.

In terms of ship building you can que up build orders of up to 99 ships/orbitals per factory at a planet. Once all build orders are completed nothing is built automatically. The number of factories at a planet are 0-4 depending on that planets population.

Population growth and resource accumulation at a planet happens automatically over time but different planet types have different population caps and will need to be actively terraformed to increase that cap.

Couriers / Harvesters/Cargo Ships / Freighters can be set on automated routes to take resources from one planet to another.

So while all of that doesn't alleviate all need to get up at odd hours if you're really striving for maximum efficiency it should certainly help.