So I started playing dawnguard and I sided with them this time. Shortly into the questline I opened a blacksmith shop for purchase and he had a set of dwarven boots of muffle in stock. Naturally I was ecstatic on finding this rare enchantment with so little searching I bought it right away. Now here's where it gets interesting, I get a note from the wizard in markarth (I can't remember his name at the moment) saying that he heard I got a set of these boots and he would pay handsomely for them. Does this mean that they will always be in stock at that shop, for every character I make from here on out? Also that blacksmith claimed he got his stock from "what was lying around." Does this mean that I could find them in fort dawnguard before doing that quest to unlock him (if for example I wanted to play with the vamp faction)?

That's from normal Skyrim gameplay and is not specifically related to Dawnguard.

ok, thanks for clearing it up, I was just wondering if it was a guaranteed boots of muffle from that shop (which is exclusive to dawnguard)

No its random leveled shop stock.

calcemo recently asked me for a exploding dwarven bolt but never once sent a letter about any enchanted dwarven armor/weapons

you would think you would get a letter from some dude who would want the Atherium item you crafted instead of just killing the [censored] that stole the girls work.