That's my theory as well. Its never sold well in the past so Sega probably didn't do a big print run for the game. Kinda bodes well if this is the case, the game actually selling out/selling well outside Japan would be awesome news
I think Sega is actually going to try this time. This is probably the most attention Yakuza has gotten in the west ever. Also I think another sign of that is the fact that both Kiwami and 6 are coming out. Had it been one or the other, I wouldn't be making this post.
And I don't blame them for undershipping 0. It's understandable considering this franchise's history.
Edit: But it's also great because 0's sales will clearly go beyond what they were expecting.