What is the difference between hub-cone type rear hubs?
There can indeed be significant differences in the manufacturing tolerances, quality of materials, quality-control processes, etc between manufacturers, or between the lines of a given manufacturer. No one would pretend that Tiagra parts are on par with Dura Ace parts (in fact people have found that Tiagra-grade chains are out of spec when new).

For all we know, the off-brand hub may be on par with Shimano's, but the point is that we don't know. There's a cyclical (heh) relationship between a brand's reputation and the quality of its products. We use the brand name as a shortcut instead of researching a product's materials, reject rates, etc (much of that information being proprietary anyhow); the reputation is built on quality, and if the quality declines, in theory the reputation does too.

There are ISO standards for hubs (and other bike parts) that limit how far out of spec even a shoddy manufacturer could go. 

The real question is not whether there is a difference, but whether you're willing to gamble that the difference is unimportant, or that the value of the time you spend researching the cheaper option to reassure yourself is less than the price difference—assuming you accept that the more expensive option is "better."