It would be possible to use a PN532 with Breakout because the PN532 uses the I2C protocol. Firmata already supports I2C so there are no changes required there. You’d have to write a new module for the PN532. See AccelerometerADXL345.js as an example I2C device. If you’re familiar with datasheets and the I2C protocol you may be able to figure out how to create the module based on the I2C documentation of the PN532 datasheet starting on page 50. However the I2C interface for the PN532 appears to be fairly complex and would not be easy to implement. I plan to add the PN532 reader to Breakout at some point but it will not be for several months as I have very limited time at the moment.
There is an alternate approach which would require wrapping the Adafruit-PN532 library and using Firmata sysex message to expose the interface to Breakout. This approach however is not well documented.
The other approach, which works now is to use an Innovations ID-12 reader instead (not that you can’t simply plug that reader into a breadboard, it requires a breakout board in order to interface with unless you want to solder directly to it’s pins). There are already examples for using the ID-12 reader with Breakout. It uses the approach of wrapping a library and using Firmata sysex messages so you could use those examples as a guide if you don’t want to purchase an ID-12 and want to try to get the PN532 working by wrapping the Adafruit library.