Maxima S - the 7gen base model - does it have a USB music port?

I don't think any of the S's come with that. Atleast mine did not. Certain SV packages may come with them.
But you can always upgrade you stereo to have one.

I have an S. There are 2 USB ports in the console under the opening.

How come I only have 1 in my 2013 SV?

On a 2016 model