See the internal diagram of the GPIO circuit for the ATmega328 for reference. ... Another possibility when you need more GPIO pins is to simply use more microcontrollers.

Regarding faster ways of using GPIO, the sysfs-interface to the GPIO-pins, while handy, is deprecated nowadays. The character-device based interface that one should use now is a helluva lot faster ...

That comes via the standard 40-pin GPIO header on the full-sized boards. But in order to shrink down the size, the Raspberry Pi Zero had to forego the header while still retaining the GPIO contacts.