What types of shops usually sell deeds?
Every shop that sells pouch items will sell a deed, eventually, except for specialty shops like the cookie vendor, the sweets vendor in Fonda Myma, and some others that open up due to events and quests.
You are correct that Aux core, cylinder, and accessory shops will not sell them since they are a bit different in that they do not sell any pouch items.
You may have to raise your dev level or do Merc missions to unlock their full set of goods.