alt Hacker NewsSC3K’s art was not “crafted pixel by pixel.” It was rendered from 3DS Max. Maxis released a version of G-Max called the Building Architect Tool that included a template with the same lighting rig that they used for the in-game assets. This tool rendered and exported the various zoom levels and orientations.
You're describing SimCity 4, not SimCity 3000. The SC3k tool is not entirely 2D, but it does mostly behave like one (with emulated voxels instead of pixels).
And while I cannot confirm what Maxis was doing internally, I am quite sure no-one was using 3DS Max for rendering game assets in the 90s considering it had just been released and well into the 2000s it was still humongously slow.