I've found that I can override it. I add the web location to the album project, then hit Update. But that fails because the hash tag has been encoded. But if I then manually change the hash tag back to #, while in edit mode for the web location, it doesn't encode it again, and it's correct in the finished album. You may have to tinker around with it a bit.
But yes, the encoding routine that jAlbum is using should not encode =, #, and ?, for exactly the reason you have discovered.