I think that some companies today are maintaining an innovative culture even given a hierarchical structure. The best example I can think of is google. Google does a really good job of allowing it's employees to have creative time to work on separate projects that truly help their business grow.
New methods arise that allow for hierarchical structure to yield innovation - this process has been very well studied for the past few decades, and people have become fairly good at it. The most innovation comes from the tech companies, all of who allow a far more open management plan.
As far as their hierarchical structures are concerned, many companies today fail to maintain an innovative environment or culture. Most companies copy every other company and make things fairly standard and lackluster for employees. With that in mind, these structures should be changed in order to promote a better workplace.
For the most part these days, when we talk about companies we are talking about international corporations and these for the most part have stayed pretty traditional in their structure of hierarchy. There are some innovative cultures and these should be applauded because they are modeling a more egalitarian way of running a business..
True hierarchies in companies are outdated in today's world. How it typically works is that there is a head of a company, followed by upper managers, lower managers, and entry-level peons. Instead, why not have CEOs work alongside line workers once a month or so? It would give owners a new perspective on how the "real" American laborer works. In small businesses, this isn't much of an issue. In companies with hundreds of employees, I think it does a lot of good if the upper crust of the company comes down to Earth every so often to see how the "other side" lives.