I don't know of any way to stop a determined and skilled person from discovering the true nature of your script (or any program for that matter) -- including any trade secrets it contains.
The best you can do with the default installation of AutoHotkey is to choose a long password and use the /NoDecompile switch.
There may be some other tips on the German forum (
http://de.autohotkey.com/forum/ ) or elsewhere about how to use a compressor other than UPX to compress the script, which may add an additional level of security. Also, I seem to remember seeing something on the German forum about a program that modifies a compiled script to make it even harder to crack.