When in doubt, turn on advanced logging and show someone the log. There might be a math problem sitting around
Quite right. Here we are:
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Looks OK to me. You are seeing 6 ships spawned. That seems about right for an early spawn. Why it chooses Mk IIIs over more Mk Is or fewer Mk IV/Vs, I don't know. Maybe Keith will shed some light on that subject. Later on, as the hacking response goes up, it will upgrade to Mk IV and Mk V ships.
It sounds from your description like you are attempting to send the Hacker into the AI system all by itself, without any support. While possible, this is difficult (as you've discovered) and not recommended.
My usual strategy is to use my fleet to completely neuter the system - I destroy all guardposts, guardians, and all fleetships. Early on, the Special Forces and Threatfleet aren't a problem, but at 90 AIP you may want to try to whittle those down as well. I also wait until both AIs have sent waves recently, so there is unlikely to be another one during the hack.
Then I rebuild my fleet completely, and send it along with the Hacker to the target system. Once there, I move towards the outside edge of the system, away from wormholes and the AI Command Station, before using the Hacker.
Then, it's just a matter of defending the Hacker foldout until time is up. I like to put a portion (1/4 to 1/2) of my fleet on FRD, so it will proactively go out and destroy the spawned ships before they can gang up on my defenders. I also use Riot starships to shield and defend the Hacker - The shields of the Riots can be very useful should a Tachyon Burst occur.
If I am attempting to hack something adjacent to one of my planets, I do as Orelius suggested, and use a Mobile Builder to build some turrets and shields, too.
An ARS hack takes 10 minutes, so you'll face about 60 spawns of ships. Most will be roughly the same strength, but in the log you may have noticed the "wild-roll" part. "Wild-rolls" are random changes to the spawn. This can be changing the ship type, relocating to an adjacent system, or greatly increasing the strength of the spawn. At the start, you only have one roll per spawn, but as the hacking response goes up, the AI will get more rolls.
Early on, when you have not unlocked many Mk II or Mk III ships, hacking can be difficult. If you try and fail (and don't die) consider capturing a different ARS or two, or unlocking some higher mark ships, before trying again. Alternately, try hacking something that finishes faster - a Fabricator, for example. Just remember that hacking response scales based on the difference between the current AIP and the current HaP, so using HaP will make later hacks harder. If this is a hack you just MUST have now, try capturing an adjacent system and building a beachhead on the target world first.
Again, however, let me say one more time - unattended hacking can be very dangerous. It is not recommended.
Here's the release notes, introducing the new hacking (in 7.002, 7.006, and 7.008).
Here's an older thread discussing the Hacking mechanics and some strategies people employ. Unfortunately, the Wiki has not yet been updated with the new Hacking mechanics yet.