They issued whatever was available. When they had it they issued it and as the war progressed it didn't matter where they got it. Holsters both w/ & w/out flaps were issued; but I believe w/ flaps would have been the predominant.
Widow; the CS started making pistol holsters out of canvas, essentially the same materials as a tarred haversack, at the tail end of the war. How many of such were made I don't know but I expect it to have been relatively few; I've heard of them and may have even seen a photo once but I've never handled or seen an original that I can recall. The one repop I saw felt awfully flimsy compared to a leather one and I can't imagine it would have held up to any kind of hard use.
As to shoes the CS imported a LOT of english shoes and made quite a few of their own via the cottage industry. I've been told at the end CS shoes were made of canvas and even some of rope soles instead of leather. That isn't terribly hard to believe as rope sandals were quite common in Texas and Mexico; I wouldn't be suprised if some CS QM bought up a wagon load. That said I've never read of shoe shortage after 63 that wasn't in the field on comapaign. In such a situation a soldier could literally walk out of his shoes. & if the QM wasn't keeping up w/ the troops w/ a decent supply of shoes the soldiers weren't going to get any except by liberal forage and scavenging.
I'm reminded of a story of the 8th TX Cav... one of the men literally stole the boots off Genl Wheelers feet while he was sleeping. It was said the enteprising soldier had to steal them off his feet because the General had heard how someone had stolen one of his Colonel's boots from his tent so he opted to sleep w/ his boots on... according to the story it only slowed the soldier down. And Wheeler, in all of his popularity w/ his men, never found the cuplrit.