Consequences of removing Launcher3's APK (com.android.launcher3) I have a rooted tablet with my own custom launcher which is already the default launcher. Are their any side effects if I delete the Launcher3's APK (com.android.launcher3) which is stored in /system/app/Launcher3/Launcher3.apk?

My device is chinese custom tablet with an RK3288 procesor, Android 5.1.1.
Don't see any issue with that. Though since you're rooted you can probably do it more cleanly with ADB as seen in this answer. If that doesn't work follow the manual delete steps listed there too.