I don't see why not, it is a matter of what the runtime allows and debugging tools.

When I talk to JEE servers via JMX I don't care if they run on as OS process, on a container, hypervisor or even a bare-metal JVM.

Likewise I get to enjoy cluster monitoring tools like Visual VM, Java Mission Control, New Relic APM, DataDog and many others, all blissful unaware of how the JEE server are actually deployed.

So I don't see why unikernels can't provide debugging access points for such kind of tooling.