No, the default autopilot bot which comes bundled with the Sanderling App does not use cloaking devices and does not react to other things in space. This is just a minimal warp to 0km autopilot, to demonstrate the basics.
Other people have published improved versions of the autopilot bot, but I right now I don’t find one with modules activation. Best autopilot I found right now was the one from @Terpla at Terpla adventures or blog-style guide for begginers - #3 by Terpla