Wonderful discution guys, I would like to thank everyone for asking such questions and thank you very much Otto for taking time answering and thanks to you Jeff, as well, for bringing this up.

On the idea of themes and plugins' UUIDs, I think it would be a nice initiative but it will be quite hard to implement since a lot of plugins in the repo won't implement it for a long time. This gets us to the idea of hashes proposed by James wich should be more easily implementable or to the idea of a tag that would belong to "private" plugins/themes which do not need/should not be checked for eventual updates, this one too could be more or less easily implemented.