Virtualization would be a part of space colonization if virtualization would be part of space colonization. Sadly, that tautology is really the best we can do.
Virtualization is a tool which can be used to solve a problem. If we have that problem, then we can use that tool. If we don't have that problem, then we wont use the tool. If there are additional requirements which prevent use of the tool, then we can't use the tool.
Virtualization will be popular if we need to have the things virtualization supports. So far, that isn't something space travel has needed. The biggest reason we haven't seen it is because of complexity. Current space software designers are big fans of simplicity. Virtualization is just one more layer that could go wrong. Also, current space software is designed on an enormous budget. When you're managing satellites whose cost plus launch can be a billion dollars, you can afford to spend the time verifying the software works. Its unlikely that you will see software which is untrusted enough to benefit from virtualization.
However, if space travel becomes truly commercialized, which your talk of "colonies" suggests is the case, then you're going to see commercial grade datacenters. On that day, you will see commercial grade solutions, like virtualization.
Personally, I don't think virtualization will be part of space colonization because we're going to come up with whatever "the next big thing" is. Virtualization solves a few very thorny problems, but it's not the only kid on the block. We probably have a lot of time before space colonization. The old days of dial up modems may be closer to our present day than colonization. A lot changed since then, and a lot will change.
If I had to pick a solution from today to appear in space colonization, I'd expect it more likely to see something like Project Midori from Microsoft. Midori went in the absolute opposite direction of virtualization. Instead of creating layers which try to perfectly encapsulate untrusted software and never let it free, Midori lets all applications intermingle in one big address space, and relies on tools to prove that one application can't mess with another. Midori was based around C#, a managed language, and they used the managed language features instead of virtualization.
The result? Midori's code runs a little slower because it's managed (and you can't fine tune managed code quite as precisely as unmanged code), but because it can safely put all processes in one address space, there's no need for expensive context switches -- all your programs can effectively run at the kernel level!
As for technologies which don't exist yet? I'd say the Internet of Things is demonstrating a major security issue which isn't solved via virtualization. We don't yet know how to secure a few hundred small devices all connected together on a network. Whatever solution we come up with for that is likely to appear in space colonization as we progress.