assuming that nobody uses it cause you don't use it is kind of.. Clearly a bunch of people don't use GPIOs. Sarcastically 90% of the SBCs will collect dust as soon as 'it's not funny anymore' so they don't even need an SoC..
As @Igor pointed out.. there are a bunch of SBCs for different use-cases.. Connectors are mostly cheap, so they solder as much as possible on it.. E.g. for the HC1 I would love to have at least an I2C bus and some GPIOs wired out.. (for some DS18b20 ore something like that to monitor the temperature).. If you want performance you'll have to pay for it anyway no matter if there are only a few or a bunch of connectors.. See RK3399 boards..
Something else you've to consider.. you need some storage for the bootloader.. Normally those SoCs can't boot directly from SATA.. you either need an SD-Card, eMMC or SPI flash.. Here as well SD-Card is just the 'most convenient' way of doing it. Not much can go wrong and in case it does.. just reflash it.