I arrive a bit late at this thread, but I'd still like to write my personal thoughts.
Just saying but... why are you building such tiny military ships? I can understand in the beginning, where any kind of ship is a struggle and all, but... you are quite far ahead in the game, research-wise. You could have surely built bigger ships.
Let me put this into context to you, compared to the real world. Your first design you posted, that 5000 tons or so ship. If we were to transfer it to wet-navy equivalent of modern days that's about ... a patrol boat? Maybe a small destroyer?
I mean, the entire earth is defended by.. 15 patrol boats?
That's a bit... puny don't you think?
To give you a comparison, a wet-navy modern cruiser has a displacement of 12000 or so tons. And a volume much bigger than that. If you were to build an aurora ship of comparative volume that would be a hull of at least 20000 tons, maybe more. For a carrier you'd be looking at a military ship of over 150000 tons.
Of course Aurora is not really the same, but I wanted to put into context how truly small those ships are, especially compared to how far you are in the game. And you could certainly say "I want to use smallish ships", but just 15 of them?
Now that I've said this, some personal considerations on the way you approach this. I want to be perfectly understood, this might not be the most min-maxing way to go about it. I always try to avoid what I consider exploiting the game system. Because many of the "exploits", a human player would immediately recognize and avoid. The AI cannot do that...
Before I plan something in Aurora, I ALWAYS ask myself: would a real nation in the real world build this, do this, trust this to defend its borders?
I am not trying to patronize you, just trying to explain how I would do it, and why I would do it, because I always try to roleplay my games in order to maximize my personal enjoyment.
1) For a jump point assault of this caliber I'd certainly , surely go for jump capable ships. You don't want to deal with the hassle of the problems jump-tenders would pose. I don't think the hassle is justified, plus you cannot retreat if things don't go well /those ships are not flexible/ etc.
2) Apart from that, you cannot expect to destroy 100 ships with 15 ships when doing a jump point assault, unless your ships are much bigger or you use the "bait ships" exploit. Basically you are faced with a decision: you either build a lot of smallish ships, OR you go with some big ships.
3) About the weapons of choice: I personally don't use box launchers on capital ships. I consider them a fighter/FAC-only weapon. I also consider them an extreme exploit while facing the AI because the AI simply has NO way to realistically defend against box-launchers spamming. It would be different against human players. That said, the point I want to make is that for jump point assault, energy weapons are a perfectly valid solution. And an extremely effective one, since Steve put in shock damage. I think people who only use missiles tend to underestimate just how... VIOLENT... high tech, large caliber spinal lasers or the like truly are. As in, ONE-HIT-KILL violent.
So all in all, I'd go with either 10-15 25000 tons cruisers with tons or armor (20-25) and bristling with Lasers of Doom, or 25-30 15000 tons or so decently armored (10-12 layers are enough) missile destroyers. Make sure to put enough fire controls as more likely than not you won't have to use the entire firepower of a ship against a single opponent.