For all of my (hobbyist-level) designs, I'd prefer to upload files as close to the native format as possible.
I don't care about my hobby designs being "ripped off" and there are several opportunities for error/non-repeatability when I go through the steps to make the gerber, drill, XYRS files, etc. If a board/assembly house will take my KiCAD files directly, I think that's convenient and one less chance for error to creep in.
For designs I was selling or otherwise was worried would be ripped off, I'd of course be a little more selective (but if I controlled the firmware, I might still prefer to send original CAD files).