I had to search a bit for that.
It has gotten a bit more complicated in KiCad-nightly V5.99 because the thickness of wires is not a constant. Thickness and and color of connection wires can be coupled with netclasses so you can for example use thicker wires (or a darker shade) for power and GND wires.
So I experimented a bit with the Junction dot size you found.
For me it did not do anything at first either.
Then I placed some new wires and made junction dots, and these new junction dots do change when this new setting is adjusted.
In the screenshot below, there are three new junction dots on the left that respond to the Junction dot size setting. Then a big junction dot I set to “500 mils” manually. Next to that and south of D485 a junction dot I manually set to a size of “0”, which now also scales with the setting above, and then a selected (light blue circle) junction dot, south of D486, and it’s properties show it’s (default) size of “36 mils”. I’m guessing that all junction dots imported from older schematics inherit the fixed junction dot size they had in the old project.
If you want to change existing junction dots then use:
Schematic Editor / Edit / Edit Text and Graphics Properties.
With this you can set all junction dots (Or use the filters in the upper right corner) either to some fixed value, or set them to “auto” by setting their size to “0”.
Setting all junction dots to “6000 mils” pretty much obliterates the schematic:
You can set them bigger, but if I go over “12000 mils” then they cover the border on all sides of the paper and you loose any reference of scale.