Are there any ways to make it so that .scpt files are not visible in the compiled .app? Perhaps by creating the class at runtime? Would that technique work for an applescript class?
if you want to hide the source text rather than the file mark the script as run-only in Build Settings
As Stefan says, you do it in Build Settings. The setting you want is OSACompile - Build Options, and you want to set Save as Excecute-Only to Yes.