Mac won't shut down, stucks at empty desktop

Hello, I got problem when shutting down Mac. Although all application are closed and the desktop went empty, there's only Finder left not responding and the only command for it was 'Relaunch' (and nothing really happened). These days I decided to shut down my mac via Terminal > Sudo Halt since that's the only thing I could figure out of.

So today I downloaded the Software Update from the App Store and it required a Mac restart. The same thing happen again, my mac stuck at the empty desktop and I went Sudo Reboot via Terminal but the updates didn't work since, it was not really an appropriate restart.

Is it bad to shut down via Terminal for many times?

And the important thing, how to fix the shut down problem?

I've been googling the same issue but turns out I still couldn't get it fixed.

Thank you.