Just to add to the "anecdotal" evidence: I watch App Store rankings for my app like a hawk, and aside from the comment about rankings not changing as often, maybe once in 2-3 hours, I haven't noticed any other changes. My app is rated very highly (4.5 for most recent version), and it's ranking inside Business category is consistent with revenue as before. Haven't noticed anything different.
Fiksu, quoted in the article, is also in the business of pay for position. We tried them once and all the downloads came from Egypt, China and similar places but none of the users actually used the app. It did artificially boost the ranking but only as long as you keep paying. I hope Apple stops these type of folks.
There is an immense amount of redundant 'crap' in app stores and I really wish they would get away from boasting about how many apps are in the app store.
I do wonder if the solution is to 'wrap' the app inside a container that reports some sort of user id/app id hash back to the store when it is fired up.