Strip /lib from installed apk
Based on my experience, modifying an APK file after the installation is not a big problem as long as you don't touch the DEX files. Especially the native libraries for other architectures than the one of your device can usually be stripped without problems as they are totally ignored after the installation. 

However there are apps that implement extra security checks (usually banking, finance, streaming apps with DRM or otherwise extra hardened apps) that performs some sort of self-test to check whether they have been modified or not. Modifying those apps will end up in a non-working app.