I think that probably depends on what your prototype does and whether the Pi is fit for production use or another option might be better.
I know a few people have prototyped with the Pi 3 and switched to the Zero/Zero-W when it comes to Production, and I'm aware of others who have prototyped rapidly using the Pi GPIO and then switched to a completely different platform entirely such as the Arduino or ESP8266 for production to reduce overheads/component size etc.
Cost certainly comes into it - 1000 x Pi 3 @ £35.ea = £35,000, 1000 x Pi ZeroW @ £13.ea = £13,000, 1000 x Wemos D1 Mini's (ESP8266-based chips) @ $2 ~= £1500.
At the far-end of the spectrum is designing and implementing your own PCB, adding an ATMEL/ARM processor and coding your own OS which may well be cheaper on runs of several thousand units.
If you're able to provide a bit more information on what you're trying to achieve, then we might be able to provide some better guidance?