There seems to be a bug in the Steinberg hardware integration into Cubase, based on this thread https://www.steinberg.net/forums/viewtopic.php?f=31&t=96537 . Here is what I can determine:
The symptom is the Steinberg-hardware-specific functionality (Device->Audio Hardware Setup and Mixconsole->Racks->Hardware) is intermittently missing in Cubase. In particular, when the Mixconsole Hardware panel is unavailable, it’s not possible to send reverb to the direct monitoring mix, which is a key feature of the UR824.
The situation seems to only occur if you’ve selected the option to not show the “Select device” popup that comes up when Cubase starts. If you leave that popup alone, and always select the Yamaha ASIO driver each time, the hardware-specific functionality will seemingly always appear. When the “select device” popup has been disabled via the “don’t ask again” checkbox, the missing hardware integration options don’t happen in any pattern I can reproduce. It may have to do with system suspend. In my case, nearly every time I open Cubase, the hardware-specific options are unavailable.
An alternate solution is to power down the interface and turn it back on. Then, Cubase will show the hardware options.
I don’t know if this is a Cubase issue or a driver issue, but the problem spans at a minimum the MR816 and UR824 interface.