While a digital pot might sound very attractive it has some hidden problems that might catch you out:-
1) Most are designed to work on voltages between the supply voltage, that is 0 to 5V. Peddles are almost always 9V so you have to get a digital pot that is capable of that voltage. This might involve doing some level translation on the control signals going from the arduino.
2) Using a digital pot involves having a common ground with the circuit you have the pot in. This is fine for just one peddle but with more than one it can lead to problems.
I once made a power supply for 6 peddles on a board. All the peddles had external power sockets, so I thought that one supply could simply be fed to all the peddles. When I switched it on there was a lot of smoke and the power supply got very hot. There were several problems. Each peddle had been designed to work with it's own isolated supply and some had the supply ground as positive and others as negative. When the audio cables were chained these had a common signal ground and shorted out the supply. Even then the signal ground and the power ground were not the same on all peddles because of what is known as "earth lift resistors". These go between the signal ground and the power ground and can minimise hum pickup. By making the power grounds common, some of them were burnt up.
So just to power all the peddles they had to have their own independent "floating" supply. This points out problems you could have if you are trying to control the pots on more than one peddle because they would need to have a common reference point.
This would depend on exactly what the circuit of your peddle combination consisted of.