If something is in something, how could it be over that something at the same time?
something is in the period that is over
in over a decade = in + [over a decade] says that something happened that either could easily happen in a decade or what we wanted to happen in a decade or what was very surprising to happen in a decade... but not exactly in a decade, rather a decade and a little bit more
This was the strongest earthquake in over a decade. = This was the strongest earthquake in [over a decade]. This was the strongest earthquake in more than a decade, which says that the last one of similar size happened a little bit more than ten years ago.
It is really used to stress something really high.
[For Google and statistical analyzes of the search results, you have to be close to an expert to confirm whether something is used in the real life usage or not. It is possible and very useful, but it is far far far far far from enough to just search for the phrase. Do not do that if you don't understand the principles. If you want I can give you the examples of how difficult that could be.]