Vinraith covered it - Hacking an Advanced Factory is very powerful, but also very expensive and rather risky.
Risky - Even at 10 AIP and positive HaP, that 15:00 hack will probably spawn somewhere between 1500 and 2000 ships, IIRC. As AIP goes up, so does the number and Mark of ships spawned. A poorly timed Hack can easily hurt the player, even if successful.
Expensive - It costs 100 HaP. That's 5 planets worth of accumulated Hacking Progress. With that same 100 HaP, you could: K-Raid for 7500 K; Hack 2 ARSs; Hack 3 Fabs; Download or Corrupt 2 designs; or get the first 85 points of AIP reduction from a SuperTerminal.
It is not uncommon where it is simply easier to just capture and protect the Adv Factory, and use the HaP elsewhere.
Doesn't it still show the mark 2 icon in the ARS after you capture it though? Maybe it doesn't and I'm just misremembering...
I think it does do that, but there's probably a bug report out, and it'll be fixed one of these days.
But for the nonce, capturing and ARS gets you the Mark I and 500 Knowledge, that's it. If you already have the Mark I, you get nothing. Same with Downloading - Already got it? Get nothing.