Learn English – What are initials

"And are they ever" means that they are to a very high degree. It is emphasising or intensifying the previous statement.

It is similar to saying that the over-represented paths are really really over represented and the under-represented paths are really really under-represented.

A simpler example would be:

Given the pitch conditions, the players should be covered in mud. And are they ever!

So the players are caked in mud up to their eyeballs.

One distinct version of the noun lay has two definitions, according to Merriam-Webster's Eleventh Collegiate Dictionary (2003):

lay n {ME, fr AF lai} 1 : a simple narrative poem : BALLAD 2 : MELODY, SONG

In the context of "In the Neolithic Age," it seems likely to me that Kipling means "tribal lays" to refer to something like "essential songs or ballads of the tribe."

In his introduction to Rudyard Kipling, Stories and Poems (2015), Daniel Karlin has this to say about Kipling's reference to "tribal lays":

The problem we have with Kipling is partly of his own making. In his delightful skit about literary rivalry, 'In the Neolithic Age' [cross reference omitted], the lesson hammered home is that 'There are nine and sixty ways of constructing tribal lays | And-every-single-one-of-them-is-right'. Yet this easygoing principle depends on an unspoken agreement about what constitutes a 'tribal lay' and gives it value. The 'ways' of writing are not the same as its purposes, and Kipling eventually found himself engaging, with a will, in literary warfare for political or ideological ends. ... We are very far here from the aesthetic principle that all 'tribal lays' are of equal validity, and from the rollicking depiction of disputes within a single literary tribe.

So Karlin thinks that "In the Neolithic Age" is a kind of satire of or commentary on the British literary scene of his own time, with tribal minstrels standing in for British men and women of letters, and with controversies over the proper direction of poetry and literature rendered as disputes over the proper way to construct a tribal lay.