Yes, e-commerce has been an issue with DNN for a long time. In my experience, however, there are actually some pretty good options. I get to work with a large diverse customerbase everyday that are using DNN in a variety of ways. The e-commerce modules I've seen my customers use most often are Catalook, AliCommerce, Active Purchase, and AspDotNetStorefront.
My personal preference is Catalook for the reasons comunicated above. It is a somewhat bloated module in that it has a TON of features that were apparently added without useability in mind. But once you get the hang of Catalook and figure out where everything is, it is a very powerful module. The documentation is okay but Nina Meiers makes up for it with catalooksupport.com, a fantastic catalook resource.
I have also got some very positive feedback from customers on the ease and simplicity of Alicommerce for simple ecommerce needs. I do not have experience with this product myself, but I do look forward to giving it a try.
AspDotNetStoreFront is just hitting stride after it had some problems with it's DNN integration. I think their main problem was that they got out of step with the release cycle of DNN (DNN broke ASPDNSF and vice versa). This seems to have been resolved and the latest version of DNN and the storefront seem to be working much better together. This is a great product if your e-commerce needs are VERY advanced. I have a significant amount of experience with this product and it has every feature under the sun. The big complaint I have for them is on the features side of things: they really need google checkout support.
Anyway, I have done a lot with e-commerce over the past 2 years or so so I thought I'd give you my quick little run down. Good luck!