No, Kirby just destroyed the source. And we know for certain because Star Allies is canonically the most recent game, and it features Void Termina, who is either partially Dark Matter or related to it. And we have no confirmation that the Waddle Dee in 64 is Bandana Dee. Also Dark Nebula, who is very likely a form of Dark Matter appears in Squeak Squad. Also Gooey still exists despite the source of Dark Matter being gone.