Why are contacts missing on some of these M.2 modules?
The contacts are missing because they're not used. The A-key variant of the m.2 spec has provisions for display port signals while the E-key variant drops the display port and adds SDIO, UART and PCM (aka I2S), I'd bet those are the ones missing, especially as this is a dual use card (as it has both the A and E key slots present, any pins that differ between the two slots have to be removed). It's probably not using the USB or the second PCIe lane either.