3d does present some additional challenges, but we decided to go this route to reduce friction for beginners who might not understand how schematics or other abstract representations map to the real world circuits they're playing with
a) You want to check that your components won't physically bash into something else you care about
b) You are designing something that operates at RF to mm-wave frequencies and need to worry (a lot) about the spatial location of the high-frequency components and nearby conductors / ground planes
c) You want to get an idea about airflow and heat dissipation on power electronics and/or modules (such as power amplifiers) that come with their own heatsinks (some SIPs do!)
Kicad and other bits of more hobby-orientated software that do a 3D render (such as diptrace) tend to do it for reasons (a) and (c). Software that does (b) properly costs hundreds of thousands of €$£ per year to rent and tends to have a UI that makes you scream with frustration at every possible moment.
or at least software that gives you an error message when it fails instead of a blank white page