What is the deal with the blackholes?

One thing seem to be sure to me, they aren't collapsed massive stars; there would not be anything left (besides some other star) in the whole star system if it was the case. They are either some kind of anomaly or the remaining effect of some super weapon used during the Colonial - Okkar war or earlier. Maybe they could be the side effects of collasped wormholes stations or the warp drive of a battleship? Many time we can see close by planets (even more obvious in sector 7), so they can't be more than mini blackholes of insufficient mass to affect nearby planets. Also, the game love to spawn stations, debris and asteroids quite close to them...
At least there must be a reason why they are so darn common
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At least there must be a reason why they are so darn common

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Dark nebula can be really tricky in this regard, especially if there are resources floating about. Have to keep your eyes peeled, checking to see if there's a mass of Dark Energy / Dark Matter near one another!
But there's always a chance of failure, resulting in the end of a run. So even when things have been made "easy," any slip up is devastating.
The trick is to go at them parallel and get the loot as you sling shot around and do a little boost when getting close and then boost away once you hit the loot. Having a tractor beam equipped makes this even easier. The faster the ship the easier it is but it works on all of them. If using the dreadnaught I would recommend the tractor beam so that you can keep a bigger distance from the actual black hole as you fly by.
Again, essentially a 100% way to collect dark energy and dark matter every time.
How about this:
The black holes were created during a MASSIVE war fought by the ancients 1000+ years ago. After being blown up, their ships became black holes, much like the guardians of Ancient temples do.
Most of the black holes dissolved a long time ago, but the ones originating from the biggest/most powerful ships are still going.
That would explain their size (or the lack thereof) and why they are so absurdly common