I was having this issue as well, my custom class wasn't showing in IDE class documentation. On a blank project (Then add custom class) it seems to work fine, but on my existing project there the custom class doesn't show.
The fix was to open the .gd file of that class, then cut everything under your class declaration
`class_name MyClass extends Node2D
...
`
Save it. Then paste back the code, resave it. This should force the documentation to refresh.