The Japanese rules technically imply that dame need to be filled in order to prevent “normal” living groups from being consider in seki, which would nullify their territory.
Filling dame appears to be the practice in at least some formal, professional situations (as seen in the video that @smurph linked above). Note that filling the dame also aids with their counting procedure, making it easier to rearrange territory into rectangular regions without worrying about accidentally counting dame.
Of course, in common practice, especially in many informal and internet games, players using Japanese rules will often leave some dame unfilled, yet don’t assert that all adjacent stones are in seki.
The rules would allow a player to assert seki (and nullify associated territory), but it also allows their opponent to resume the game and fill in dame to remove the grounds for that assertion. Hence, actually making such claims (perhaps in a futile attempt to win a lost game) would seem ridiculous and even insulting.
So are players technically violating the Japanese rules by not filling dame, while regarding adjacent stones as not in seki? Perhaps, but not in a manner that changes the result of the game, and only as an informal way to avoid extra moves. I view it as the players basically coming to the mutual understanding that they won’t waste time with actually playing inconsequential stones, but still pretend that they have filled the dame for the purposes of determining life/death/seki and counting the score.
However one views this practice, I think it is way too strong to say that it is evidence that the written 1989 Japanese rules are nonsense. The rules are not rendered invalid simply for not codifying an informal shortcut.
As another example, in the video mentioned above, we also see professional players rearranging stones (while even breaking border lines!) in order to make manual counting easier. This method is not technically sanctioned by the rules (even if you allow some rearranging, breaking the borders would clearly render territory invalid), but no one seems to object since it is understood that they are not really changing the score.
To be clear, I do think that there are significant drawbacks to the Japanese rules (mainly revolving around the complexity of life/death adjudication), but I don’t think that dame being left unfilled is a source for substantial criticism.