I'm in the same situation of writing a technical Master's Thesis. I did not thoroughly read through design guides ... but from my point of view:
We have to differentiate technically correct typography from design. The first one deals with how to properly set equations, plots, and that kind of things. For instance: ISO-31 is a standard that describes how to properly set variable names, function names, constants, etc.
I have read many books for my studies and many of them even fail this simple criterion. As a student, reading equations in these books is a pain. You never know if 'c' is a variable, physical constant or super-special-subscript because it was improperly typeset. A good nomenclature helps but turning pages all the time is time-consuming. For instance, constants are set always upright (same for greek symbols that are constants).
Therefore the first thing to care about: Are all your plots, equations, etc. properly typeset?
For anything that goes beyond, there is probably no extra credit and you should reconsider if it is really worth it to spend your time for having a fancy design. In addition to that, most examination offices still ask for documents that are compatible with pre-computer-era guidelines (1.5 line spacing and such).
For a simple but good design you may want to:
- Choose a 'good' easy-to-read-font (with serifs) with a matching math font
- Ensure a consistent appearance of all figures and tables (e.g., same font)
- Plots either use same set of colors (online version) or dotted/dashed lines for a print version.
- Layout according to proper book design (enough white space, not 'fullpage'), a suitable documentclass should take care of this already (book, scrbook, memoir)
- Make 'nice' tables according to common guidelines, i.e., no vertical lines. Have a look at the package
booktabs for beautiful tables.
- Depending on your exact field of study, you may want to have a look at
siunitx. This LaTeX package is a good start to properly typeset units.
From my point of view, a 'good design' for a thesis (!) must not stand for its own good but instead ease reading and understanding it. I somewhat doubt that fancy chapter headings and that kind of things are any good to this. Perhaps they even distract some readers.
The question also is on how LaTeX specific you want to have your recommendations. Another book to recommend for sure is: "Visual Display of Quantitative Information" by Tufte. Tufte's books are quite famous and therefore a LaTeX package exists to reproduce his style, e.g., 'tufte-latex'.
When it comes to typography, there are a lot of things to debate (paper type, paper format, choice of fonts, color, type area, margins, page break, line break, units, formulas, tables).
Perhaps you can indicate a specific topic the guideline should focus on. As you saw, there are complete books just focusing on fonts :-)