I finally get rid of annoying Nepomuk Indexing problem by enabling Nepomuk Search on both my laptop and desktop. Even though it's a CPU-consuming process, it's worthed since i hate to have that error message displayed at random time during my presentation at class.
People or my students who looked at the error message might said that Linux is broken or no different with Windows (error-prone) or whatever reasons to discredit Linux. In fact, it's only KDE-related problem, not entirely Linux's fault. Linux is just the kernel anyway, but most people don't understand this basic principle.
I have to say that enabling Nepomuk Search does have a drawback, mostly if you have a moderate CPU specs. It will rise your CPU utilization as it will try to index all metadata on your desktop. Depending on how much data you have, the process will take some time to complete. Once it's finished, the process will be much lighter than it used to be.
In my system, i disabled Strigi, since i don't use KDE search feature. I use locate or find in command line which is fine with me. It's also faster and more effective IMHO. Enabling Strigi will cause you more CPU resources. Wasting resources for something that you don't use is silly enough for me.
Anyways, i still hope that future KDE release should have the same behaviour of KDE 4.5.5. Even by disabling Nepomuk, we won't have to see those Nepomuk Indexing error messages. Well, it's just one of my wishlist for next KDE release. I hope they see this blog post somewhere