Is that always the case? I know at least some of Nintendo's player's choice line for Wii u used different ISBNs compared to their regular line.
Most of the time it is the case. Of course there are exceptions as you noted with Nintendo. But in my past experiences with PS2; PS3; and Xbox 360, their Greatest Hits and Platinum Hits always carried the same UPC / catalogue numbers when the content was identical to the normal release. Now, if the content is different -- as was the case with Silent Hill 2 GH which featured additional content not found in the normal release -- then it will obviously have a different ISBN / UPC / catalogue number.
Of course things can change this current gen (I doubt it); but just in case it doesn't, it doesn't hurt to secure the "blue label" versions of the games you want. The worst that can happen is that you have to do a return if the UPC changes.