Well, honestly I think they didn't think at all. One developer just thought that the technology needs a file to store stuff in and dropped it in ibdata. And if you ask him, he asks you back who would ever want to delete files from that directory.
Perhaps this is from before it was called InnoDB, maybe the codename was "Innovative and Brilliant", so this would make sense then.
Edit: According to Wikipedia, the company that invented InnoDB is Innobase, so this would be where "ib" comes from. They have been acquired by Oracle, though.