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.