I checked on the other side (not sure why it hasn't occurred to me to do that), and found this. There's a bolt under all the grime on the left, and on the right side it looks like there was a bolt but it was sheared off or something. I wiped away the gunk that was covering it and there's something there.
I was in agreement with the idea of a through bolt from the right side til I saw the right side photo. Now I wonder what is there on the left.
If it where a factory installed bolt you should see some type of clean area or shiny area where the head of the bolt was before.
If you clean it off better maybe you can tell.
Also if you find another bike with that engine take a look.
I noticed it was missing because there's a slight leak. I ordered a new one from the dealership (6mm x 50 flange bolt, stainless steel) and it'll be in this weekend. In the meantime, I'll probably crawl under there with some Purple Power and get it cleaned up.
it might be a chore to get it out of there but probably a drill and e-z-out will get it, maybe from the right side for easier access if there is more room , it may just screw all the way through.
If it is a 6 mm it is only about 1/4 inch diameter so be careful tightening the new one or the head may snap off that one too. I thought it looked like an 8 mm size by the photo, maybe not.
Update: the bolt arrived at the Honda dealership, and I cleaned out the underside a bit more. There's something blocking it partway into the hole, and so I'm just going to live with the slight leak for now.