How can I have 2 differents frequency on the 2 DAC outputs on an Arduino Due?
I don't have experience with this, but what you can do is:


If the frequency of DAC1 is x times faster than DAC2 to calculate the delay time based on the fastest and for DAC1 changing in every loop, while changing DAC2 only every DAC1/DAC2 times.
Vice versa if DAC2 is x times faster than DAC1
However, if there is not a simple ratio between DAC1 and DAC2 than you have to use the fastest speed of the two and use for the slowest an approximation... 
Or use a higher significant fixed speed for i use a simple linear approximation between two points of the wavetable.


E.g. assume the speed is 10 times too fast for DAC1.
Suppose i = 100.. you should use the following points in the waveform: wave[100/10] and wave[100/10 + 1], so two consecutive points.
Assume the first is 10.0 and the second is 20.0... for the 10 increases of i (because i is running 10 times too fast) you can calculate for values of 

 i     : 10.0 +   0% of (20.0 - 10.0)
 i + 1 : 10.0 +  10% of (20.0 - 10.0)
 ...
 i + 10: 10.0 + 100% of (20.0 - 10.0)


etc. 

Note this is called linear interpolation.

You would have to check how many numbers per wave form table you need to get good values for different frequencies/speeds and what 'fixed' frequency you need to use for the delay.