The short answer is yes, a GTK# application would be accepted into the AppCenter repositories assuming it met the rest of the review process (basically that it doesn't do anything questionably legal or mess with the system).
The other thing to be aware of is that it must be a GTK 3 interface, not GTK 2. I'm pretty sure that'll be the case by default with GTK# though.
However, the part where you're possibly making life more difficult for yourself is the fact that I don't think I've seen any C#/Mono/GTK# apps in the AppCenter yet, so there won't be any handy examples of how to set up your build tools and packaging files so that Houston (the build/testing server for AppCenter) can automatically build, test and publish your app.
It's not an insurmountable problem, I'm sure someone somewhere has packaged a GTK# application for debian based distros before, but you're less likely to get quick help and support as it's something that the elementary team will be more unfamiliar with.
Have you had a look at Vala (the language used for elementary OS itself and the included apps)? The syntax is incredibly similar to C# and you could consider tools like Glade or the nightly builds of GNOME builder via flatpak (that now include built in Glade) to design UIs. That said, I'd recommend at least trying to build UIs in code without a designer as it teaches you how things interact much quicker.
Hope that helps! Good luck with your app development, I hope to see some of your apps in the store in the future!