I would use the one I mentioned in the article - DAP clear silicone Sealant for Doors And Windows. Or you can use Clear GE Advanced Silicone Window & Door Sealant, which I have used in other projects that will set outside. Using one for Doors and Windows means it's rated for being exposed to the weather.

What kind of glue should I use for this project?

That was the sealant I used at that time (that project is a few years old). It worked very well and was the best available at the time, but I've recently switched to the GE Advanced Silicone 2 for Windows & Doors. It's a more updated product that dries quicker and is a little better in rainy situations (outdoor projects).

And I put it on as a dot on each individual penny. Either one is fine, but the GE products seem to get upgraded more often.

I like the gemstone tumbler idea!!! I've only had one fall off right by the finger hole, but I do bring mine inside in the dead of winter when the snow starts flying. As for spraying with a sealer, I did not. Without sealer it should last about a year before you'd either want to re-clean them (I just used a toothbrush to brush on some of the cleaning solution) or you can embrace the tarnished look 🙂 Whatever sealer you use, make sure it's OK for outdoor use. I know Krylon makes one called Make It Last that specifically states it's for outdoor use.

Garden centres offer copper tape for just this reason. It "shocks" the little buggers!

I'd love a coin floor too!