Regarding the various versions of GNOME and KDE:
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Short answer is: yes, you need them.
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Long(er) answer: in Linux there are several package formats that you can choose from when installing software. There are pros and cons to each of them but the bottom line is that they work running in isolation from the rest of the system. To achieve that, they need to install additional "runtimes" or "frameworks" for each version of a particular program. In this particular case, it looks like what you're using is Flatpak package format which is one of the most popular ones.
This is all to say that if you have installed software using the Software Store, you probably don't want to delete them.
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Long answer: Packaging formats and their use in Zorin OS
Virtual Machine Manager is a front-end for managing virtual machines. Typically you see it used in conjunction with something called KVM (Kernel-based Virtual Machines) but it can be used with other types of hypervisors.
It's strange that you have it installed, since VirtualBox doesn't install it. But in any case, it should be safe to uninstall as these are different programs after all.