If a Mystic Swordsman attacks a DD Warrior Lady or Assailant that is face down, what happens? If it is Mystic LV6 does it negate the effect and return it to the top of their deck?

DD Warrior Lady or DD Assailant is destroyed by the effect of Mystical Swordsman. (MS Level 2/4/6 would all work the same but Level 6 can then put the warrior back on the top of their deck)

The term "Negate" which you used is not appropriate in this example. None of the Mystical Swordsmen "Negate" anything.

While DD Warrior Lady or DD Assailant is F/D, they have no active card text or ability. Hence if they are destroyed while F/D, they are essentially effectless monsters.

~S

Just wanted to make sure. This brings up another question. If I set a DD Lady and it is attacked by say Jinzo, doesn't DD get it's effect and can choose to remove or not?

In that situation yes you would get to remove, and here's why:

Your opponent declares an attack: His Jinzo attacks your face-down DD.
Nothing is activated in response to the attack, the attack now goes through to damage calculation.

DD is flipped face up, Jinzo's 2400ATK beats DD's 1600DEF so DD is dead.

Now that damage Calculation has been applied, DD can activate her effect and remove both monsters.

HOWEVER: If DD is attacked and destroyed, by Dark Ruler Ha Des, Dark Balter the Terrible, Guardian Baou, Terrorking Archfiend, Ultimate Obedient Fiend, or any monster equipped with Wicked-Breaking Flamberge Baou, DD does NOT get to use her effect. She also cannot use her effect if she is in face-up defense mode and is attacked by Ninja Grandmaster Sasuke.

The thing is, with MS 2/4/6/Paladin of White Dragon/Sasuke Samurai/etc, when you attack a f/d DEF mon with them, you destroy them WITH THEIR EFFECT and NO damage calculation being applied and such, so if you attacked a f/d DEF position D. D. Warrior Lady, you're declaring an attack, but D. D. Warrior Lady would be destroyed as if you used a Raigeki Break on her or something, in which case, she could not activate her effect since she never actually "battled" with anything.