If a unit is stunned alone at a unit, does it still conquer? I (as defender) stunned the attacker, then he hidden blade me and is alone, does he conquer?

Yes, the unit still conquers the battlefield.

According to the official rulings and the Resolution Step (Rule 444), a unit being Stunned only prevents it from contributing its might to damage during combat; it does not prevent the unit from establishing control or conquering a battlefield if it is the only unit remaining there.

The Sequence of Events:

1. Showdown Begins: Your opponent moves a unit to your battlefield (becoming the Attacker). You are the Defender.
2. Stun Applied: You stun the attacking unit.
3. Hidden Blade: Your opponent plays Hidden Blade, killing your defending unit.
4. Resolution Step:
   • Because your unit (the only defender) was killed, there are no defenders present to deal damage or block the conquest.
   • Rule 444.2 states: "If no Showdown or Combat is staged at this location, the player with Units remaining here Establishes Control."
   • Rule 444.2.b confirms: "This results in a Conquer if that player has not yet scored that Battlefield this turn."

Key Ruling:

An official FAQ specifically addresses this:

"A stunned unit conquers an empty battlefield. Stun only prevents dealing combat damage, but does not affect conquest of empty battlefields."

Because your opponent's unit is now alone at the battlefield (even though it is stunned), they successfully Conquer and score the point immediately.