The dialectic version from the American Memory site includes:

"Dey's some, dey's black an' thin, An some, dey's po' ol weddas, but the res dey's all brung in."

Translation:

There are some, their black and thin, and some, they're poor old wethers, but the rest, they've all brung (come) in.

The meaning - as I get it - is "all the good ones are in, but there are some "black and thin ones" and some "wethers" that didn't come in.

A "wether" is a castrated male sheep. Common practice is to castrate nearly all males, since they're troublesome - to both the ewes and to the shepherds - if this is not done. Traditional lore is that the wethers produce inferior wool, and as they have no value for breeding, they are generally destined to be mutton. Relatively worthless animals.

Black and thin carries a similar connotation - worthless - because of the lower value of black wool.

The derivative term "bellwether" refers to a (usually) wethered male sheep that "leads" the flock. When sheep are turned out to "range" it is uncommon to mix rams with the flock. A wether will commonly be used, although the bellwether term is applied pretty generally to any "lead" sheep. The main purpose of the bell is for the shepherd to be able to locate the "bellwether," on the assumption that the rest will be nearby.

The phrase "The Master ... look out in de gloomerin' meadows, Where de long night rain begin," I would read, to mean 'looked out at the darkening meadows, where the long night rain (is) begin(ning).'

In this version, it seems more fitting to interpret that the Master is wanting the sheep in as darkness is coming on and it is beginning to rain, than that he's going out in the morning to count the dead (which often is the result of having wool-laden sheep out in a heavy rain.)

John