You are not the first player to complain about this issue and the answer is both obvious and obtuse at the same time. Simply, stop exploring so much. There is no win condition that requires you to explore the entire galaxy. Odds are, there are plenty of systems where you need to build up your infrastructure, clear out spoilers, handle NPRs and so on. The problem is that you think that you must keep exploring constantly and the management of the survey ships is grinding you down. The answer is not to add more automation to handle it, the answer is to stop exploring for a period of time and then resume exploration once the systems you have already surveyed are fully under exploitation. Also, 30+ ships is a massive number for your survey fleet. What I do is either use a handful, like 4-6, big all-in-one survey ships, or then a bunch of smaller, specialized vessels that work in tandem to do a single system at a time. And between systems they take breaks. That way each system survey is special, I name the interesting planets/moons/comets/asteroids, medals are awarded and a nice little ceremony held at Earth for the commanders. This way it's a story event that you enjoy doing, rather than "oh no, yet another survey order to assign". If you ever feel like that, simply stop surveying and focus on something else for a while.

There are only 2 reasons to keep surveying as much as possible, as fast as possible, and that's because you want to encounter something spicy or you desperately need a specific mineral and you've been unlucky so far. Don't kill the fun of Aurora through your own actions! Also, if you think I'm daft for suggesting this, that's fine. Last time I gave this advice to another player, they had a little temper tantrum about how I dared to tell them to change their playstyle and posted some nasty stuff. Just ignore me if you feel that way, we don't need to start a flamewar or anything.

If you want to maintain a fleet, use Divide Fleet as Primary and Return to Entry Jump Point as Secondary (or Land on assigned Mothership if using a survey carrier). Once they are gathered, reassemble and move to next system.

It's generally easier and more flexible though to use individual survey ships.

Anything that's attached to a fire control, has an active sensor lock, and is within the range of both the beam weapon and the fire control (accounting for any ECM/ECCM) can be used to shoot at anything.

The only caveat I can think of is that if you have a beam control that has a PD setting, and you use it to fire on an enemy ship, it will be unable to fire at any incoming missiles in that same 5 second tick (or however long your recharge rate is).

Sorry, i probably wasn't clear.  the ship has beam fire controls set to single weapon and PD, so i'm guessing that your first answer applies and they cannot target ships.

It does have active sensors and the ship does show on target list.  I should have put a regular beam control in them to switch the lasers to in situations like these, oh well thats what Mk. II is for. 

Thank you Andrew.

Apparently I was not clear
Any Beam fire control can target any enemy ship in range . so you should be able to shoot at him, the pont defense settings have no bearing on your ability to shoot at ships

Sorry, i probably wasn't clear.  the ship has beam fire controls set to single weapon and PD, so i'm guessing that your first answer applies and they cannot target ships.

It does have active sensors and the ship does show on target list.  I should have put a regular beam control in them to switch the lasers to in situations like these, oh well thats what Mk. II is for.  :)

Thank you Andrew.