I haven’t even noticed… Maybe you’re right, but I dunno. Besides, it’s not like you upgrade mercs that often…
On PC (Windows), you go to the Campfire, at the lower right corner (to the left of the game’s settings button) there’s a field with a green ‘plus’ icon, a number indicationg your total Renown and a Mercenaries icon. There’s also a tooltip about renown if you hover you pointer there. You click there, just like the first time, and convert your excess coins to renown if you will.
PS See the picture:
https://hearthstone.blizzard.com/en-us/news/23852694/24-6-patch-notes#MC%20UP
[UPD]
Actually, the game asks a confirmation for upgrading equipment, but not a skill, as I’ve noticed with Rattlegore. This is indeed very strange and inconsistent… And I don’t remember whether it has always been that way.