D.S.
I'm so sorry for your loss. I, too, am dealing with a similar tragedy this week. My best friend, my 8.5 year old dalmatian, Tino, passed away last friday from a very aggressive cancer. My son will be 3 in two weeks.
Tino was going through chemo so my son also knows that he was at the doggie doctor a lot. Here was here at home shortly before Tino passed so he could say goodbye, but didn't really understand that and was at a friend's house when the vet actually came to put my pup to rest.
He knows that Tino is not around right now, but like your son, waited two days before he really asked for him. I think he is finally understanding that for some reason, Tino really isn't here. I kind of believe my son thinks he's at the vet. He mentioned picking him up this week. And he said yesterday that Tino is coming back and I had to gently tell him, no, he's not. Today, he thought we were taking Tino on his daily walk when we took a stroll and I reminded him that wouldn't happen again.
I think it will take time and I'm not sure that at the point he's old enough to understand for real he will even remember Tino.
I will say that I am not taking it well! Truly, heartbroken. And it's ok for my son to see my cry. I think it helps him know that everyone gets sad sometimes. And it may let him realize in a small way that although he doesn't "get it" something has happened in the family.