First, in all benchmarks but two, Java performs just as well as C/C++/Rust, and in one of those two, Go performs as well as the low-level languages. Second, I don't know the details of that one benchmark where the low-level languages indeed perform better than high-level ones, but I don't see any reason to believe it has anything to do with virtual threads.
Modern Java GCs typically offer a boost over more manual memory management. And on latency, even if virtual were very inefficient and you'd add a GC pause with Java's new GCs, you'd still be well below 1ms, i.e. not a dominant factor in a networked program.
(Yes, there's still one cause for potential lower throughput in Java, which is the lack of inlined objects in arrays, but that will be addressed soon, and isn't a big factor in most server applications anyway or related to IO)
BTW, writing a program in C++ has always been more or less as easy as writing it in Java/C# etc.; the big cost of C++ is in evolution and refactoring over many years, because in low-level languages local changes to code have a much more global impact, and that has nothing to do with the design of the language but is an essential property of tracking memory management at the code level (unless you use smart pointers, i.e. a refcounting GC for everything, but then things will be really slow, as refcounting does sacrifice performance in its goal of minimising footprint).