Can I automate my system survey?

You can queue orders.

This can be applied to any order, holding SHIFT when assigning orders will put them in a queue. I don't think there is a way to automate the process entirely but stacking them in a queue will help. The only problem with this is if there are any hostile forces the queue will be disrupted and won't continue until you re-assign. One good thing about the system is that if there are any anomalies you can research them and it won't break the queue it will just place it at the top to be done first and then continue.

I will take a look at home tonight if there is any method of automation and update this if I find a solution.

There is a Feature called Automatic Exploration that is unlocked by the Physics Technology Automated Exploration Protocols. This will allow your Science Ships to explore the galaxy while controlled by AI (though it will still need a scientist, as I recall). It also increases your surveying speed by 25%.

The only prerequisite for this technology to appear in your Physics tech choices is that the current game year be 2210 or later. Here is what it looks like in-game: