Also, if an open source is popular enough to the point a unique VID is needed for proper driver support, I will say this project will easily get fundings to go commercial (just like RedHat).
The fee is $5k if I recall. As others have mentioned, if you are planning on making a real product, it's something you can roll into the cost. Although I completely understand the difficulty of someone just looking to sell ~100 devices.
I wonder if there's a way to allow a "Bring-your-own" VID? As in maybe switches or something to set the VID by the purchaser?
And also, to find the device from the OS API, you sometimes have to submit the VID/PID of the device you are looking for. Example: http://developer.chrome.com/apps/usb.html#method-findDevices So changing it on the fly might be a problem (not sure, maybe once open they won't seek it again).
Following a link on the internet it look like they actually have a prototype VID/PID, but you have to contact the forum and sign some boilerplate (saying you won't release your product with the proto numbers) to get it.