Dublin streets were covered in horse dung in Joyce’s days, as we can read in the Eumaeus episode:
On the roadway which they were approaching whilst still speaking beyond the swingchains a horse, dragging a sweeper, paced on the paven ground, brushing a long swathe of mire up ... (16.1770-2)
So it looks like a straightforward, if metonymic, appeal to cleanliness, when Molly puts her exasperation about religious sceptics into a reference to cobbles.
Gifford is not quite satisfied with this explanation and suggests:
’Cobbles’ is dialect English for encrustations, lumps, and blemishes as well as for cobblestones.
Dent, in Colloquial Language in Ulysses, however, is not convinced and legitimately asks:
Even if a valid definition, how does it fit in the context? (275)
Translators’ efforts avoiding the term “cobbles” mirror the difficulty, too. Georg Goyert’s German translation in 1927 has the slightly vague “den Dreck abwaschen” (wash off the dirt), echoed in the French translation by Auguste Morel of 1929: “se fair enlever leur couche de crasse”.
It is surprising to see that Dent, who is usually painstakingly thorough in his scrutiny of the resources of the OED, missed the most obvious explanation provided for an age of ubiquitous coal fires:
Cobble 2. pl. Coal of the size of small cobble stones.
Cobbles are what we in London should call good round coals, being the larger lumps picked out of what they call the sleck or waste small coals.
John Farey Gen. View Agric. Derbyshire (1815) vol. 1 p. 187
Cobbles (between 4 and 6 inches in diameter) seem to have been mainly used in kitchen fires:
"Fetch me first a trug of cobbles,"
Said the cook; and, undismayed,
To the collier sped the culver,
And a trug of cobbles prayed.
Saint Nicholas (1882) August, p. 818
This extract from Fun magazine confirms the dust nature of kitchen cobbles, and Punch indicates that they are not of the same class as "selected nuts":
My king of the forest [...] went for four suburban artists who were engaged at the moment in my coal-cellar in making leonine studies from him at the nominal rate of eight pence an hour. The fact was, I have been since assured, that one of these artists, in spite of my warning, took it on himself to re-arrange Gumbo's tail — a liberty which even that meekest and mildest of beasts would not permit. He had already allowed the same artist to curl his mane, but no sooner was his tail touched than, with a gummy roar, he shook the dust of the kitchen cobbles from his crest, and, as I have said, went for the artistic quartette.
Fun (1881) vol. 34 p. 159