If you're familiar with LaTeX then that's a good point to start setting your thesis with. With LaTeX you can specify a few parameters like margins and then your layout class will compute the rest for you. Perhaps take a look here. (I used the KOMA book LaTeX package to set my thesis.)

Other than that, if you want to use inDesign (why?) then what parameters do you have? Paper size? How many levels of heading? Illustrations, tables?

I'm not familiar with LaTex, but thanks. I started to use InDesign for fun, and because I want to learn it but that's not exactly related to the issue. I'm only asking these things because I'm not very familiar with page layouts in typography yet.

So my original questions: What line spacing and margin do you think works well with Palatino Linotype, if only one sided pages are used. There are two levels of heading and figures every 3-4 pages that take 1/2–1/4 of the page.
As for the margins I tried top: 2cm, bottom: 3.2cm, right:2cm, left:4.2cm so the written text snaps to a golden ratio grid.
Am I on a good path? I can't decide between a line spacing of 1.5 or 1.25 (1 looks too crowded and I find it hard to read for 40 pages).

Thanks!

Page size?
Type size?

A4, 12pt

If you already have enough text to fill two facing pages, I suggest to play around with different settings. From past experience, seeing the print will give you a much better idea than going by numbers. The line spacing will also determine the text block size: tighter spacing, smaller block; and then the text block size can be placed differently depending on header and footer and folios.

If 12pt is not negotiable, then this already decides the line measure (characters per line) which should be about 2 alphabets.

Bottom line, there are many different factors and personal taste at play here. Print them out and let your personal feel and taste guide you :-) When you found something, perhaps post it here and then people can discuss tweaks and improvements.