Yes. Ubuntu is recommended. We are internally developing OMNeT++ on Ubuntu. Some of us inside a VM (on a windows Host). So it's definitely working.
I think processors are 64-bit capable since ages (like 2004?). The main limitation was that OMNeT++ 5.0 itself came with a 32-bit compiler (even on a 64-bit windows host, this was limiting the model address space). OMNeT++ 5.1 now comes with a 64-bit windows compiler, but INET and simuLTE still was not tested in 64-bit mode on windows.
Long story short, I'm definitely recommending running omnet in Linux. You will get 64-bit address space and faster compilation times. Yes, even inside a guest VM, the compilation is faster than on the native (windows) host system!