I have the same issue. “Audio Hardware Setup” is missing from Devices menu.
I am using a Steinberg UR824. This sort of issue should not be happening in a Steinberg application.
Please see the workaround posted here:
I reran the latest UR824 Tools setup. When I load Cubase, and again get prompted to choose my Audio Interface, I DO NOT CHECK “Do not ask this again”. I select my interface and continue into Cubase. As long as I do NOT select the “Do not ask…” box here, the Audio Hardware selection is visible in the Devices Menu! I’ve closed and reopened Cubase several times, I think it works! 
I sincerely thank whomever discovered the problem was related to that opening Cubase, interface prompt. I’ve been in several Posts and cannot locate the thread that offered the above work-around. Give it a try, if it bothers you to click on an audio input Head Phone icon within the mixer. 
Asking the same question here, just in case you missed it in the other thread!!
G’mornin’, Gents & Ladies… Does anybody know whether this issue has bee resolved in Cubase 9? I’m on Cubase 8.5.2 with a MR816x, and have been plagued by this bug for quite some time. Would gladly purchase Cubase 9, if I knew this “feature” is reimplemented.
Me too!
There is a new driver available. Looks like it fixed BOTH problems, the disappearing Hardware Setup menu/dialog, AND the disappearing hardware tab in the mix console. Limited testing, but looks like it’s working properly AT LAST!
Thanks for the info, rtorstrick… Downloaded and installed the new driver. Seems to be working, so far!! I guess we’ll know if it stays this way, but so far it’s looking good!!
The same problem is back again in 9.0.10 with 1.7.8 driver 
I might be wrong but I guess the issue starts if I first power off MR816 and the shut down Cubase. Steinberg please correct the driver again.
I still suffer this issue with latest drivers and Cubase 9.0.1. 
Did it really get cured??? Or were people just lucky in not having it happen for a while?
The 1.7.8 driver sorted it for me and still good …Cubase 8.5. My question is when and if I upgrade to 9 will the problem return?
I have a vague feeling that 1.7.8 cured it in 8.5 for me too but hard to be sure as I don’t use the Hardware Setup window on a daily basis so it may be that it was still disappearing and I just hadn’t noticed.
I’m running 9 and it seems to be working correctly.
Had the issue with Nuendo 7.1.3 two days ago.
A reboot fixed it.
Direct Monitoring is also not working when it does not show up. Really annoying when you get to the studio in the morning and have a voice over session right away.
There is an easier way IMHO. Set the Driver to “No Driver” ASIO driver in the studio setup > VST Audio System. then restart Cubase. Now select MR as your driver.