They all have to work (at least to an extent) using only x1. It’s part of the PCIe spec.

Missing pins are actually extremely common. If your board has a slot that’s x16 (electrically x8), which is very common for a second video card, take a closer look. Half the pins in the slot aren’t connected. It has the full slot to make you feel better about it, and it provides some mounting stability, but it’s electrically the same as an x8 that’s open.

USB the protocol, or just uses a USB cable? If it’s not using the protocol, the cables are a cheap way of getting cables of a certain spec.