In older versions of Simcity, the radiation left behind by a nuclear
power plant explosion slowly decayed away over hundreds of years. I
could never verify whether or not this will happen in Simcity 3000.
Running unattended at the highest speed I could get it to run at, it
would have taken a week to run 500 game years; I've never been willing
to perform that test.
For practical purposes, the fallout symbols are now a permanent feature
of your city; you'll have to build around them. This isn't a bug, that's
precisely what the game designers intended. This is a risk you take
when you build nuclear power plants, and if you do decide to build one
anyway, it's a strong reason to do everything you can to prevent them
from blowing up. Never overload them, replace them before they get too
old, and keep a fully funded fire station right near the plant to put
out any fires that break out.