From the Wikipedia article it seems ones' complement representation for signed integers is mostly obsolete, but they mention some Unisys systems, namely the UNIVAC 1100/2200 series as still supporting this representation.
Do the latest systems in the Unisys Clearpath series still support and use ones' complement?
Since they use intel chips, do they require an emulator? How performant is this?
Are there C compilers targeting this architecture?
I don't know the facts.
What I do know is that when you have mountains of running software, it is really hard to pull the technology base out from underneath.
I'd make a pretty big bet that it still does ones' complement math in any instruction set simulation (or chip implementation) that runs the software.
You can build an emulator on top of any other CPU. UNISYS asked us to help them do that back around 2007 with an explicit target of a hi-reliability 64 CPU x86 system. Then there was a financial crisis so the project didn't materialize for us.
They've obviously done a great deal of engineering since to keep it alive. And yes, people still run these.