For example, we are now moving away from nuclear due to the dangers associated, so we only have it for less than 100 hundred years.

The half-life of uranium is 4.5 billion years. Let's say civilization of earth is wiped out and someone visits the planet a billion years from now.

Could they tell that there was something here just by the levels of uranium, assuming that say we only used it for 200 years before moving fully to clean energy?

A billion years is a long time. But if they came in a million, they probably could - if not from radioisotopes, then just from observing that the surface layer composition of metals doesn't fit any reasonable geological model. We dug up a lot of stuff, and while this initially concentrates them, as our works decay, they get dispersed into the environment, and I doubt a million years is enough for them to reintegrate back into the crust.

But wouldn't those substances be buried deep in the soil 1 billion years later? Or in the case of Earth with all the plate tectonics, entire plates could be already inside Earth's mantle.