Yes, the utilization for these supercomputers sits upwards of 99%. There's a lot of research into supercomputer queueing that helps maintain this high throughput. Larger jobs usually take days to weeks to run.

There are separate debug queues for smaller development and test jobs that prioritize latency over throughput, and this is a main source of inefficiency (but, as someone who develops on supercomputers, trust me, it's necessary to make them usable).

As for the efficiency of the codes--there are a lot of barnacle-encrusted Fortran codes in astrophysics, chemistry, and elsewhere. Some of them probably contain plenty of inefficiency, but the cost of re-writing them is high. Oftentimes either the people writing the codes aren't interested in maintaining good software quality (because they're focused on the science) or the incentives aren't aligned to re-write code that's already established, but from the 80s (re-writing old code is generally not how one gets a Ph.D.). But they do very important things, like simulate nuclear fusion or the interaction of chemicals in the atmosphere that create weather patterns and storms, so it's very important to run them.