Unfortunately, snapshot~ doesn't seem to send data at a rate which enables clean signaling of arduino pins. When it comes to audio anything, I find that outputting signal is necessary, as outputting control values just cannot keep up with audio. If you are looking to make a square wave generator that is controllable from puredata, the best way that I have found to do this is by using a combination of arduino, a DAC chip and an op-amp chip. Also, you'll want to use at least a 12 bit DAC, such as mcp4921 or mcp4725, as 8 bit DAC lacks the ability to tune the output fine enough to stay in tune with standard tuning. For opamp choices, you can pretty much take your pick. They all do pretty much the same thing, though you will find that every opamp has it's own unique sound quality. I really love the gritty sound of the CA313. A very good and popular sound for opamp VCO is the tl072 or tl075. There are tons of schematics out there for how to configure a square wave vco with opamps. You would just modify the components to fit the output of your DAC.
Next, you would send your controller values from PD to the arduino and have some code in the ar'dweener to handle communicating with the DAC. You can then add all sorts of fun stuff to your board like digipots, opamp buffers, VCAs and so on to make envelopes, LFOs etc.
If you don't want to track down additional chips (usually ordered from china being the only way to find them, cheap though they tend to be,) but want to have square waves being output directly from the arduino, then you would still be better off having pd send control values to the arduino and then let the arduino handle the signal generation to it's pins. For this purpose, you may want to look at the tone library or the mozzi library. Teensy boards have some expanded audio capabilities as well, but teensy boards are a bit expensive for my taste, as you can get a freakin raspberry pi with a full linux operating system on it for a fraction of what it costs. Still, teensies are great and extremely handy for these types of applications if you dont mind dropping some extra money. I try to build everything to work on cheap arduino clones just for financial and practicality sake.
I have code and patches that I have written to control these types of circuits for many DACs and digipots with SPI and I2C protocalls... let me know if you'd like to check them out for some guidance.