As a hardware developer (like arduino board etc.) does one have to license PCB's files under GPL if the included software uses GPL licensed parts?
No. From a copyright perspective a hardware layout and a software application are completely independent works and their licenses don't affect each other.
Also I'm not fully understanding GPLv3 about Tivoization part. So If I use GPLv3 software parts, Do I obligated to design PCB that allows future re-flashing for end users?
What the Tivoization part of the GPLv3 means is that if you have the possibility to re-flash the PCB, then you must not employ techniques that limit that possibility to you alone, but anyone who can make the correct connections to the PCB should be able to re-flash it.
If you design your PCB such that it can only be flashed once, or that the software resides in actual ROM memory, then that is not a problem for the GPL license.