@panometric
Depends what "large numbers" is. For say 100 you're probably be using the development modules (WiPy, LoPy..) , in that case flash over USB is perfectly doable. You can connect multiple expansion boards to a USB hub and flash in parallel, we have a script for that.
For larger deployments you're probably using the OEM modules (W01, L01 etc) in the case we recommend having programming pins available. All you need to program is power, UART TX/RX and two pins to control Reset and GPIO0 (P2)