Sooo ... what is your question? You obviously found the threads about that topic, so you already know that the limit is arbitrary and might be lifted on request. Opening a thread here is not the way to make such a request.
Can't your game engine compile asset archives? The way I remember those threads, the explanation was somewhat along the lines of deterrence of low quality exports of certain engines that give a crap about html5 games and would work heaps better as a downloadable game for the user.
I do not know very much about html5, but thousands of file system level files seem just very wrong for this technology. This is even garbage on a normal harddrive. I seen stuff with over 10k files after extraction. This is just not done, or should not be done. And there usually is no need at all for this type of shenanigans. As a development version to debug, ok, files away. But as a distribution version? What kind of tech illiterate made the decision in that engine to work on file system level to organize assets for deployment to the player?