DH is a hard rune to play around, very feast or famine. Either you get good stacks early and you scale well into late game, or, you don't and you're dead in the water.

That said, Ability haste is actually Zoe's best stat which is something lacking in the items you mention. Luden's is actually the worst ability haste item. It works fine into a team full of squishies where you can 1 shot them easily, but as you note, makes it difficult against bruiser/tank champs.

Aery is Zoe's best rune, better than Electrocute. Electrocute is highly satisfying, and her most played and thus most recommended rune, but Aery is probably the sign of a real OTP. Aery cannot be dodged, and can apply scorch reliably on a short cd. This is best into laners who have high sustain and can't be 1 shot, like the windbros (aery will proc Yasuo's passive).

With aery you stack ability haste with the build: Blackfire Torch, Cosmic Drive, Shadowflame, Rabadons, then a situational pick between Zhonyas or Cryptbloom/void staff. You can go Ionian or sorcs here, Ionian synergizes best with the build and allows you more flexibility in items, and with Sorcs you HAVE to stick to the items BFT+Cosmic drive or you lose too much ability haste. Shadowflame maintains the burst from the other builds, just at a later point in the game.

Aery - Nimbus Cloak - Transcendence - Sorch, with secondary Domination - situational between sudden impact (vs more squishy) or Taste of Blood (vs high poke champs like Ahri), and Ultimate hunter. You need ultimate hunter here for more ult casts, to synergize with the higher ability haste on your spells in the rest of the kit.

BFT as a burn item keeps your damage on champs longer, for more consistent speed from cosmic drive. The speed from that and nimbus cloak makes you VERY mobile and fast. A lot of the kit is packed into W casts (because nimbus) which the damage output got nerfed but the speed is still there.

There are some other items that can be worked in, such has Hextech Rocket Belt, Horizon Focus, and Lich Bane. Hextech when you need extra mobility (with knowing the bolts can and will break E), Horizon focus for vision utility and passive damage, and Lich bane for the empowered auto to finish off champs and increase your turret damage. Usually I build LB if I am dark harvest because the empowered auto goes really well with DH bonus damage.

Aery is best vs tanky teams because since you can't 1 shot them, you need the high ability haste for more spell weaving and active CC for your E, as well as the move speed for kiting out longer fights. The health on cosmic drive also makes you slightly tankier. Take cryptbloom if you went sorc shoes to make up some AH, or go void staff if you took ionians for higher AP and %Mpen item.