Probably goes without saying but the last line of defense is not deploying your software publicly and instead relying on server-client architectures to do anything. Maybe this will be more common as vulnerabilities are more easily detected and exploited. Of course its not always feasible.
It has been annoying seeing my (proguard obfuscated) game client binaries decompiled and published on github many times over the last 11 years. Only the undeployed server code has remained private.
Interestingly I didn't have a problem with adversaries reverse engineering my network protocols until I was updating them less frequently than weekly. LLM assisted adversaries could probably keep up with that now too.