Are there any Male to Female DI2 wires / exetensions?
No, there are not any male-to-female "extension" wires available for the Shimano Di2 E-Tube system.  You can use a junction as you said, or you can use the two-port ANT module.  You could also modify an E-Tube wire to lengthen it yourself, if you are handy with a soldering iron.