What you're doing sounds good. You could try software I2C just in case?
var i2c = new I2C();
var nfc = require("PN532").connect(i2c);
That'll be able to use the internal pullup resistors which may work if the PN532 doesn't have any.
Another issue could be the voltage. IIRC the PN532 needs quite a bit of power to get its coils working - it's possible that the 3v CR2032 doesn't supply enough power.
In that case, you'd just have to:
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