For an HTML5 game, it should be able to load within a certain amount of time (even on slow connections). This isn't NewGrounds where every game has a several-minute loading bar (or longer).
If folders are being counted as 'files' then that may be a bug in the system. However for now it may be useful to offer a downloadable option in the interim.
I feel that instead of a 'number of files' limit that itchio just have a 'file size' limit for HTML5 games and devs offer a download option for larger projects.