Weighing in on this, I would prefer that markups not be directly visible, but it is not all that important.
On the issue of markups being high or low, there can be many reasons for having various markups. Other than the pricing consistency McTrivia mentioned, it is often necessary to make an investement that does not immediately return profits. That is actually the Shapeways model, partly subsidizing model costs during the growth phase until momentum brings prices more in line with what we are used to in mass production. Personally, I underprice my smaller models because they are not going to be a major source of income anyway, and take very little time to edit. I consider it advertising for my design services, which is how I actually make money. I have been giving away 3D-printed promotional items for years and it has worked very well. People don't forget it, and I've had many customers come to me as a result of seeing one of the items I gave or sold to someone else. The extreme version of this is what China is doing to us right now. By dumping electronics and other products on us at a loss they have wiped out all the competition and taken the whole market.
The other side of that coin is that many people associate price with quality, and artificially inflated prices are actually a central element to aspirational branding. Do you think a Starbucks coffee actually costs anything near the $4.50 you pay for it? No, it's part of the branding and it depends on the context of the sale and the type of product. Since 3D print production costs are already high, this is a tough sell.
The only reason I support concealing the markups is that most people don't have even a basic understanding of these issues. I would rather we just talk about it openly so that people don't feel inclined to do the creepy analysis of people's shops that Mctrivia describes.
Btw, I still sell 3D prints at retail stores, and while I don't sell many items, I do move stacks of business cards, which is just as important.