Yes. All resources in will be included in the apk. The apk is the installed application; there's no point at which the resources are copied elsewhere before running it. You can confirm this by installing your app on a Nexus 10, then using adb to make it emulate other dpi targets. Even though you've installed the apk when the device was at a xxhdpi, relaunching it at mdpi doesn't kick off another install, the mdpi resources are already there.
A solid strategy for reducing the size is to simply not use large images when they're not necessary. I use conservative 9-patches and substitute xml drawables for shapes when appropriate. If you've done everything you can and you're still concerned with the apk size, you can create multiple apks that target different dpi points.