Hi Zimi,
Integrating Arduino with Scriptographer should not be too hard. You could even embed Arduino directly in Scriptographer, as it's based on Java just like Scriptographer. Embedding Processing would be a bit harder, as it needs a graphical interface, which currently interfers with the Illustrator interface. Future version might fix this.
But if you want to run any of these outside of Scriptographer and have a connection between the two, you could open a TCP socket between them through which you send commands, e.g. using Processing's Client / Server classes:
http://processing.org/reference/libraries/net/Server.html
http://processing.org/reference/libraries/net/Client.html
In Scriptographer you could then either do the same, by using the classes from processing.net.* through the JavaScript to Java bridge, or implement one using the standard Java net classes.
See you soon in Basel.