Is the I2C link rate limited by the SCL frequency?
I am thinking of setting the link rate to 500kHz or 1MHz with the SCL frequency = 400kHz.
Which link rate (500kHz or 1MHz) is better?
Table 2 in the LTC4331 datasheet will be the guide to follow. A 400kHz SCL corresponds to the Fm I2C Class, which means a Speed Index of 5 or greater.
Let me edit this to add a detail... The clock width is reproduced by the LTC4331 pair. If Speed Index 8 is chosen (1MHz Link Rate), the SCL coming out will have the width of a Fm+ clock. It may be too narrow for the remote I2C devices to interpret at there probably isn't any advantage to do it. I'd recommend picking Speed Index 5-7.