Well prefixes can separate the threads somewhat, but it's just a lot easier to have sub sections in my opinion. I don't see the disadvantages of having them. I want to go and look at theories; I look in the theory section, if I want to go and discuss the upcoming installments; I look in those specific sections.That's way there's a prefix for each thread, that way we will always know what that thread will be about. I honestly see the less subsections, the less clutter.
I don't think it's a bad idea as such, but I just like the convenience of the sub sections, just my opinion though.