Why do strict designs of theses exist?
Why do many universities require strict format on theses,


Actually, sometimes the requirement is not as strict as you would think, and they do accept some variety. Also, if they provide a template for you to use, that's not the same as not accepting anything that diverges from it.


  when the most important thing in them is the content? 


That's the most important thing to you, or to academics interested in the content. It's not the most important thing for, say, the librarians, or the secretaries who have to process the theses.


  A beautiful design will make a good thesis better, and a bad one worse. As long as the content is guaranteed by the writer, why restrict their desire to make their work, at the very least, clearer? 


Your question comes off as being rather self-centered. The university is (or may be) trying to make a collection of theses beautiful, not a single one. Don't publishers have series of books or journals with uniform design? Don't streets have rows of buildings with uniform or uniformly-changing design? ... and those streets in which every person built their own house, according to their own means, with different architects who have no sense of context and are wrapped up in their own ego (or with no architect and just some construction company just putting up whatever is currently cheap and fashionable) - are these the beautiful streets? Rarely.


  If academia is a place for creativity and logicality


Logicality? Ok, my friend, you are clearly not ready to graduate if that's your view of academia. You need to "bake" in there for a while longer and lose some of this naivete of yours...


  where are the creativity and logicality in strict designs? 


I think I've suggested a reasonable argument as to why a university might want a uniform design. Well, it's either that or some administrator deciding on that arbitrarily, the same way the government has a bunch of standard forms. Which is it? Who knows.