It is a problem. Most people will find it very hard to load your game in a browser with that many files, let alone play it. Can't help but notice that the downloadable versions are hundreds of megabytes in size. A game that big really needs to be played on the desktop, not online.
That said, I've let our admins know about your problem (can't remember if we talked before, sorry). The limit can be lifted if you really need it. But I urge you to reconsider.