Can you submit app to the App Store using Xcode 9?

You probably mean Xcode 10 beta. Xcode 9.4 is the current stable release, and still works on Mojave. Of course, if you're nuts enough to be using Homebrew or MacPorts on Mojave, you'll probably be forced to at least have Xcode 10 beta installed on the system and configured as the active version of the command line tools to install packages again.

Just to expand on that, normally you can’t submit to production from a beta OS (such as Mojave right now) even if you use a production Xcode.

My personal recommendation based on a lot of experience is to avoid beta releases of everything as much as possible. Stick to production stable releases if you need to support production builds of your app. There’s a reason the phrase “bleeding edge” exists.

As you say, 'usually' - Using a release Xcode in conjunction with a beta macOS -has- set off flags during submittals in the past, so I'd be surprised if the combination of Xcode 9.x and macOS 10.14b would be allowed.

That said, I recall anecdotal reports that such franken tool combos have succeeded in the early days right after a macOS beta dropped, but once the backend was reconfigured to know about it, the curtain went down.