Were all/most/much the Native American political and ethnic structures that existed before the European colonization destroyed by diseases and what was the connection of the tribes later encountered(Iroquois, Lenape ect) to the pre Colombian tribes?

I think the framing of this question doesn't help. In the area I've studied, the Northeast (who were neighbors of the Iroquois, or Haudenosaunee), recent scholarship in this topic emphasizes the continuity of governance and culture over time after contact.

The Wampanoag of Massachusetts, for example, were decimated by disease around 1619. Yet they remained a powerful local polity whom the English settlers who highly dependent on. Archeological evidence, European accounts of the 1500s (from trading, exploration, fishing, and slave raiding missions), and oral tradition points towards a relative stability in governance and culture before contact and afterwards. One political structure, the sachemship (think of these as one of the smaller levels of polities, a collection of a few towns) and the paramount sachemship (what the Wampanoag were, a collection of various local rulers led by one paramount sachem) may have been strengthened and emphasized because of English settlement in the region and the effects of disease, but there is no evidence that political structures were destroyed. Even going farther out West, where groups like the Comanche in Texas and other polities becoming less sedentary were relatively recent developments, the political structures upholding these groups adapted and changed before European contact, because of warfare, trading, and indeed disease, but political systems only ever came close to being destroyed by European and later American forces.

Recommendations since I'm not at my desk:

Silverman, This Land is Their Land.

Bragdon, Native People of Southern New England, 1500–1650.