Ruth,
The markups, as with most any retail merchandise, is subject to corporate decision makers. The bolts are bought for "X" amount and the markup that follows will be based on quantity ordered, saleability of product, trends, the manufacturer, and things of this nature, all basically put into a mathematical formula that computes the markup value per product. Some margins are bigger than others.
Generally, the smaller specialty shops have a higher markup because it cost them more to buy the bolt. Factor in all the expenses of running a shop, rent, insurance, payroll, supplies, theft, wasted merchandise, advertising, utilities, well, you get the picture, it adds up to a tidy little sum, which we as consumers feel in our pockets and can't justify.
Hope that helps, at least some.