It is up to you whether you would like to change the substrate, but after 3 years I would be inclined to. It can trap lots of nasty stuff like phosphates.
Be very careful replacing it though, because disturbing it could release harmful gases into the aquarium.
I would reccommend replacing small portions at a time, maybe 1/3 at a time. If its fine enough to siphon out I would do it that way, since then you minimize the release of gases. And then just scoop in the new stuff. I would wait a couple weeks in between substrate removal sessions.
-Diana