Perhaps not a RTOS per se, but latency is an issue for some HPC applications. Or not latency per se, but unpredictable latency among different nodes. The basic problem is that many large-scale simulations do frequent global barriers. So if one of the nodes is a bit slower because, say, the OS decided to schedule out the application and run ntpd for a fraction of a millisecond before switching back to the application, all the other nodes will wait. The more nodes, the higher probability that something like this happens, and application scalability takes a hit.

The term you want to search for is "OS jitter", lots of papers on that topic.