Beads in bags
Meredith Harmon on the Paternosters list on Yahoo turned up a painting that answers this question -- at least for one instance. It's a painting of the Annunciation to the Virgin Mary, painted by Gerard David somewhere in the late 1400s. It's now at the Metropolitan Museum of Art in New York: for some reason it doesn't appear anywhere on their website, although the other panel from the same painting, showing the angel, does.
Just visible in the bottom right corner of this painting is a cloth pouch with rosary beads spilling out of it. Here's an enlargement (as always, click on the picture to see a larger view):
The beads are gold-colored but don't look metallic; my guess is that they are supposed to be amber or glass. Just visible above the edge of the pouch in the back is a decorated silver gaud or marker bead of some sort (not much detail is visible), followed by ten smaller beads. The string is dark, probably black. On the other side of the loop we can see nine beads. Both strings run through a round, decorated silver ball at the far left, and it looks like they are knotted together on the far side.
The pouch has two black drawstrings that appear to end in knobs (knots?) and there are matching black tassels at both bottom corners.
It's a bit difficult to estimate the dimensions of the pouch and beads, because they are in the foreground of the painting and the perspective is a bit strange. It looks to me as though the beads are a little smaller in diameter than the Virgin's fingers, perhaps around 10 to 12 millimeters in size. The silver ball is about twice this size. My guess is that it may be a pomander.
Using the bead as a rough unit of measure for the sides of the pouch, the bag looks like it might work out to be about 8 to 9 inches square. That's a bigger pouch than would be needed just for the beads.
Another painting by Gerard David, probably painted around the same time and now at the Detroit Institute of Art, provides a clue. This second Annunciation is a more compact painting, and the Virgin is at a rather different angle, but the bag in the foreground is identical, right down to the folds and wrinkles (except that it's blue this time).
Those who have commented on these paintings suggest that both bags are intended to be book bags. Looking at both paintings, the bags do seem to be about the right size to hold the book that Mary has in front of her in each case.
The earlier Merode altarpiece (also at the Met) by the workshop of Robert Campin has a very similar bag under the book on the table, and here too it looks to be just about the right size to hold the book. This purse also has two drawstrings, and it looks as though one ends in a round, thread-covered button, and the other has a longer string ending in a tassel (though most of it's hidden under a slip of paper). There is a contrasting colored lining and some decoration around the mouth of the bag and down the side seams. This painting and its two wings have all sorts of delightful details in them if you ever get to see them close up -- carpenters' tools in Saint Joseph's shop, a towel with striped borders and fringe, a vase, two keys, and a candlestick, among others.
(The only beads in the Merode altarpiece, however, are held by one of the donors of the painting in the left wing of the tryptych. These are a long straight string of perhaps 100 smallish red beads, with white-headed black tassels on both ends. I have a small picture of this, but I'd love to have a detail shot of the entire string to see if more details are visible.)
So from this evidence, we can suggest that beads, at least some of the time, were in book bags. It does make a certain amount of sense to carry one's devotional beads in the same bag as one's devotional book (which is probably what the pictured books are). And we have some pretty good pictures of what the book bags were like, if we want to create a modern reproduction, to carry our own books, beads, or whatever we like.