Although the Arduino Due is powerful, it's stil not nearly as powerful as a computer. Both memory and CPU cycles are very limited. If the total memory used for all synths exceeds the available memory in the Equation Composer, the unit will not generate any audio after being programmed. If the CPU of an individual synth exceeds the maximum CPU cycles avalable, then the synth may continue to generate sound, but the controls will become unresponsive and you will be unable to change programs.
The amount of memory and CPU available is very difficult to compute. The largest synth that hasn't exceeded the CPU limit contains 9 modules. In other words, programming is farily limited.
Input smoothing requires CPU. If you're running into CPU limitations and using input smoothing, try removing the smoothing.