Thanks for the info. I have had Shortcuts issues in the past and Evernote Support's position is "That shouldn't work anyway so we don't support it" (even though they make the Evernote actions available in Shortcuts - except on the Apple Watch of course).
I believe I know why this API limit thing happened. My legacy V6 Windows 10 version of the Evernote client stopped syncing a few days ago. I avoided upgrading to V10 because of the things I've heard about it and because I like the V6 interface so much. Plus I have a really old slow Windows PC and was worried about performance of the client. Anyway, since I couldn't use the Windows client any more, I started using the web client from a Chrome-based browser. That's when my Shortcuts stopped working and I got the API Limit message. I logged out of the web client and exited the browser, and then the Shortcuts started working again. So somehow the web client is constantly pinging against this hourly API limit, even though it doesn't prevent the client itself from working. I have noticed that under Account Settings / Applications, "Chrome Web Clipper Extension" (which I don't actually have installed) is listed dozens of times. So maybe it has something to do with that.
Anyway, I finally upgraded to the V10 Windows client. It's working okay and is not too slow, but I still prefer the V6 interface. So now I'm not using the web client and the Shortcuts and IFTTT integrations seem to be working okay. Hopefully that will last...