Originally there was no suffix for the first document. I think this change was made for consistency with New File In Project. (I'm also didn't think the file suffix should be ".js", but that was also changed for consistency.)

Anyway, yes, I could imagine storing this number per-project instead of globally. But maybe we should all agree once and for all about what the behavior should be for both New Document and New File In Project before tweaking one or the other.