It's been over a year since Apple required all app updates to offer a 64-bit binary. It would appear that the firm now wants to warn you when you use an app that doesn't comply with the rule, or more specifically, a 32-bit app that hasn't been updated since before June 1, 2015 when the rule was enforced.
In the iOS 10 beta, opening a 32-bit app will display a warning that the app isn't optimized for iOS 10, that it hasn't been updated to 64-bit, and that it "may affect overall system performance".
The phrasing that is used is strong. It's not just telling you that this 32-bit app might be slower than 64-bit apps. It's telling you that it might affect your entire system, even when you're not using the app.
Presumably, the message only displays on a 64-bit iOS 10 device, which would be all of them except the iPhone 5, 5c, and fourth generation iPad.
Of course, this is only the first iOS 10 beta, so anything is subject to change between now and when the full version is released in the fall.