Since it's in the far future, it's assumed the protagonists from Mother 2/Earthbound are just dead from time. Pokey/Porky did make repeated trips to the past, but this is what caused him to age rapidly and also become immortal. He's not only stuck in the future with no way back, but he can never truly die. The Absolutely Safe Capsule has trapped him in an eternity of solitude from the rest of the world.
As for Smash, it isn't akin to the Mother series story line aside from character appearances. In reality, there's no way Ness and Lucas would ever meet up since they come from different time lines. By the time Lucas is even born, Ness is long dead not just from old age, but from the destruction of the old world when everyone traveled on the White Ship.
On the subject of a sequel, Itoi himself stated there wouldn't be an official sequel. He's finished with the series as a whole, and since his daughter is older now (part of how the series began as Mr. Saturn are based on her and the concept of innocence), he has no desire, or see's any point to continue anymore than he has done. However, in an interview, he has stated that he wouldn't mind a sequel not made by him, as he would be most interested in playing it himself. This fact, along with the fan-made title Mother 4 that has been in the works for two years now(?) leaves many Mother fans eager for the game; Despite it being a fan-made title. The developers of Mother 4 have revealed there will be reference and connection to the other Mother titles, but it was also confirmed we wouldn't see any old characters. They also specifically stated Pokey/Porky wouldn't make an appearance. Hope this answers everything.