I am not as experienced as some of the other modders that have commented here but I've been modding ever since the beginning of this year and am now actively working as part of a dev team for a pretty big server and the modding wiki was a big part of my introduction to modding for Vintage Story so here's my two cents:
Fully agreed, the navigation at the moment is certainly an experience. There's some pages I never would have found without someone in the mod development channel from the official discord pointing me to it (VTML for example). Using the wiki without saved hyperlinks quickly causes you to lose track of where a certain page that was only hyperlinked in one very specific other page was to be found. I think establishing a similar concept to the "Playing the Game" section on the main page https://wiki.vintagestory.at/Main_Page , with very direct and specific bullet points would be an incredible improvement already. Since it would result in way too large of a table if everything was stuffed into one, differentiating between Code and Content would be the a good starting point in my opinion.
Overall, taking a look at the current "Modding the Game" section on the Main Page, I think it needs to be more strictly divided between JSON and C#. Everything JSON should go under a "master" Content table and everything C# should go under a "master" Code table. Looking at the current table "Modding the Game" again, the different options are not descriptive enough to tell me what I will find in there just by reading the hyperlink text. For example, the quickstart guide should probably go. It's not *bad* per se but I think it's name is counterintuitive as it'll attract people to it simply because it's called a "quickstart" guide. Modding Basics, Asset Types, as well as VS Model Creator should be rolled into an overall Content tab, with the community showcase for what mods have been made in the past getting it's own, separate tab - something along the lines of "community mod showcase". At the moment the Modding Basics is a link leading to a mod showcase of existing mods as well as more links that lead to the actual modding basics. Asset Types is just pure Content/JSON material so it doesn't need it's own specific icon. The Content Mods and Code Mods sections are good for what they are but renaming them to something more descriptive like "Content Introduction" & "Code Introduction" might be more telling of what you'll be lead to when clicking the link.
I could ramble on more and more and get hyper specific for certain pages and will do so if it's something that would help but I'll leave it at this for now
Here's a crappy example whipped up in LibreOffice Calc of what I had in mind when talking about JSON/C# or Content/Code separated tables (I couldn't think of many things that made sense off the top of my head for the filler but just the categories should give you the right idea I had in mind)
(This is more of a general (and minor) pain point from my end but having C# dependent mods be referred to as "Code" when it's also a general term for the act of creating mods and such has caused me to double back when talking with others, especially those who have no modding experience, very, very often. Anyway I digress.)