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.

Indeed, the most important thing in a thesis is the content. But not everybody who has to write a thesis is skilled in graphic design, formatting or typesetting and therefore, if given free rein, the final formatting might well be pretty awful.

Furthermore, uniformity in theses undoubtedly helps those marking them, by ensuring all the content is in the same place in every thesis (for example, there is a title page with all the student's information, an abstract, table of contents etc). This is particularly important for things like bachelor's theses where one person will probably be marking more than one submission.

Finally, what constitutes a beautiful design may well be interpreted as ugly by someone else, so by having uniform formatting, the chance of unconscious (or conscious) bias against the work due to its appearance is reduced.

In short: we shouldn't judge a book by its cover.

When part of your job is to be a reading a lot of some particular media (which could be books, journal articles, web sites, or theses), it really helps to have a fixed format that you can depend on. If I know where the summary, conclusions, methods, contacts, etc. are, it saves a lot of time that would otherwise be spent trying to decode the format for each individual paper. I can prioritize, determine what parts to focus on, where to start, what to skim, where to flip if I have questions midstream, etc. Trying to read an article in a wildly nonstandard format may take twice as long or longer.