Digital clock with 3 nos SAA1064

You are correct, there is a possibility that pulling up the SDA/scl lines to 3.3V might not work. I have never tried this. You will need to test the circuit. Being quite old, the saa chip may not have been designed to work with 3.3V signals. But connecting the SDA/scl lines to 5V could damage the 3.3V MCU. If your testing shows that 3.3V does not work reliably, you will need a logic level convertor module to translate the MCU's 3.3V signals of SDA/scl to 5V for the saa chips. These modules are easily available and cheap on eBay etc.