I recently had sucess connecting one of those PN532 modules via I2C directly to the DE10-Nano, using the same header as used by the realtime clock. The header provides 3v3/GND/SDA/SCL so all the required connections. Just make sure that the jumpers on the module are set to I2C mode, mine wasn't in this setting by default.
To know if it is being picked up by the system, use the i2cdetect command to check the address, 0x24 is the default address.
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i2cdetect -y 2
0 1 2 3 4 5 6 7 8 9 a b c d e f
00: -- -- -- -- -- -- -- --
10: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
20: -- -- -- -- 24 -- -- -- -- -- -- -- -- -- -- --
30: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
50: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
60: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
70: -- -- -- -- -- -- -- --
The tapto.ini had to be updated to use a custom connection:
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connection_string="pn532_i2c:/dev/i2c-2"