I think you have a great idea -- specifically, that it should be possible to sneak single ships through defended jump points in order to perform commerce raiding or other 'submarine'-type missions -- that was presented with terrible mechanics (jumping to somewhere else).
I would LOVE[/b it if Aurora better simulated submarines (though, personal preference, early submarine of the type that spend 90% of their time on the 'surface' and only 'submerge' to attack or evade).
We have cloaking, but it doesn't seem to achieve the job on its own. I do wonder if there's enough in the form of things to raid, however. Planetary PD in C# should be enough to stop a few subs from effectively striking planetary assets, which is fine. Shipyards are a good target, but shipyards are rarely without ships that'd intercept a submarines worth of missile fire. Fuel harvesters are probably a good strategic target, and I imagine most folks just leave them alone, maybe with a civilian PD on 'em. Civilian shipping losses don't have much impact outside of RP purposes, so the effective value of raiding might be low. There's not much in the way of military supply convoys. Still, that's less relevant than being able to try and do it anyway, I just wonder if there's anything we can do to add options. Stealth military insertions, maybe?
As far as how to breach these points go, perhaps some sort of emissions sinking, coupled with special regular-space engines to allow you to capture the thermal signal from them (and make it cost prohibitive), and a heatsink line of tech. When a ship is sinking emissions, its completely blind, and heating up. Get too hot, you can take internal damage from it. Cooling the ship lights you up, more/better heatsinks extend this time. Combine this with cloaking to reduce your active cross section, and the jump dispersion that already exists, and you'll be invisible to passives, and hard to detect with actives. But stay 'submerged' too long, and it'll kill you, and the mission tonnage spent on special engines and heatsinks means getting caught will leave you easily outgunned for the cost.
My hope is the heat mechanism and heatsinks provides an upper limit on how 'big' of a submarine you can feasible achieve at a tech level, between the cloaking and the tonnage limits. It also means that submarines don't become feasible until you develop some technology, so it is an investment to develop this stealth tech, atop the manufacturing costs of the special parts. I can't imagine thermal sinking hasn't been proposed before though, so I look forward to seeing the flaws in this