Thanks

There are two loopholes to exploit when going for a very high score even with relatively weak ships. The first is that Elite Fighters replenish when you save+quit the game and then continue. The second is that in nebula sectors, every beacon is an ion storm when overrun by rebels, so they only charge 2 shields even in sector 7. If you upgrade your ship with reactor bars and only power your weapons and very few other necessities (using only half your reactor bars), you have overwhelming weapon power against a weakened enemy. Weapon Pre-igniter helps as well

Also recommended are Cloak and Defense Drone with Drone Recovery Arm (but sooner or later, you will run out of drones, so it's better to not use any drones for very high scores).
The same loopholes still exist in AE, only non-nebula sectors are a bit more challenging with their antiship batteries, but with very powerful and fast (Pre-igniter) weapons and appropriate augmentations you probably can also hop around in normal sector rebel fleet territory at leisure, but I haven't tested this yet. Not sure if I'll go for more high scores in AE, I hardly have time for basic playthroughs, unfortunately...
At least I finally cracked the 6k barrier in AE!

Changed playing style to super risky and was crushed accordingly three times in a row with the Man of War, first time it was unwinnable. Had 20 hull and four engines in sector 1, when I met an autoscout with an Artemis, which got into my cockpit and set it aflame (2 flames). Next missile hit the weapons and then the engines (also aflame), then I had repaired the cockpit. Next missile again into the cockpit, two flames. My slugs had to heal themselves before going fire extinguishing again, took all missile hits in the meanwhile, repaired the cockpit, got a missile into the cockpit again, and as the autoscout had apparently at least 10 missiles to spend and each one hit, my 20 hull ship was destroyed. Breach I regularly missed (when available) and Dual Laser didn't get through two (? not sure, at least they never penetrated) shield layers... good fight!
The fourth run was blessed with lots of lucky drops and events, and I had some luxury problems in deciding which weapons to choose. Almost felt like cheating, as I upgraded Hacking to level 3.
Took one hull damage during the third incarnation, but luckily I had Hull Repair for the third flawless victory
Man of War: loss, loss, loss, win (1/4)