best tool for 3D math is complex numbers. most languages removed support for them.
If your gripe is over programming languages not having support for 3D math, then I think that should be expected. Most languages try to keep their standard libraries small, and their built-in types smaller. A language that has built-in support for such things would be incredible niche. Maybe JAI is what you're looking for? I'm not sure if that even contains built in support however.
Even the posted primer suggests you can skip the section that mentions complex numbers.
What do you use them for?