Материнка - is derived from "mother". Motherboard - материнка or материнская плата if you want to be official. Материнка is kind of slang, although almost everyone would know of this word and use it.

Why use матерника for the herb? As the sentence you provided mentions this herb has the capacity to heal specifically female deseases. That would mostly mean things related to giving birth. So the herb helps become a mother.

Ладанка is not really about an amulet, it's about "ладан" or "incense" in English. So it's logical to assume that the herb smells somewhat like incense.

Душища, мацердушка, душмянка are the same as ладанка because it also relates to the herbs smell. Дух is archaic for "smell" in Russian. There is a well used word derived from "дух". It's душистый. It's mostly used to describe something with a pleasant smell. E.g. душистая сирень, душистое мыло, кофе etc.

Пчелолюб - this one is obvious, it says that bees like (love) this herb.

Мята лесная - it's either the herb looks like mint but grows in forests or smells/tastes like mint and grows in forests.

Костоломка - Hmm, hard to say. It's either the herb can relieve pain in your bones or that it can be the cause of it.

Зеновка - no idea here.