Every port increases the wiring complexity on and size of the mainboard, as well as the bill of materials.

It's probably minuscule for something like 3.5mm audio (even though analog noise on the board might be a concern), and the computer already needs a DAC/ADC for its built-in speakers and microphone, but when in doubt, I'd rather take a port that I can convert to another using a cheap adapter than a fixed-purpose one I never use.