I don't think this will actually be a big problem in the wild. Yes, there will probably be thousands of Github projects with developers' first attempt at a component, all sharing names like x-button, but how likely is it that you'll be using them in a real project? Let alone using two and having a problem with them colliding. Most developers who create a component that provides significant value will expend the effort to think of a unique prefix and name, I think, and will have enough knowledge of the wider dev space to know what's already taken.
For the situations when a collision does occur, I think it can be better addressed by the kind of community consensus already discussed, and by good tooling, than by trying to design clever namespacing mechanisms.
If we speculate about the future of web components, I imagine that *most* components used in real projects will be hosted in one of two ways:
1. On the same server as the web site/application
2. In a few CDNs that specialise in component hosting.
In the first case, since the developer has control over the component resources, it's possible for them to manually resolve any collisions simply by changing the element name. I imagine people will write Grunt tasks and other build tools to automate this, and conventions for packaging components will evolve to make it easier. Component libraries could also provide download tools, akin to those used by libraries like jQuery UI, that let you download a build with a specified prefix.
In the second case, the hosts themselves can enforce unique names within their own registries, and with a bit of collaboration, amongst themselves as well. They can also provide ways to mitigate collisions. For example, if I ran a CDN called
componenthost.com, I might offer two versions of each library, one with a convenient short prefix, and another with a longer, more likely unique one. So, the Polymer components might be available with a pol- prefix at
http://componenthost.com/polymer and with a polymer-project- prefix at
http://componenthost.com/polymer/full, or some such.