Oh lord I remember those. I searched for them but I didn't see them where they used to be, not sure if they moved them, I missed them or if my game glitched.
Everything in the game is as the same as it was in the original game 11 years ago. The only difference in chests is the contents inside are shifted, especially the ones with dalmations. I got ALL the puppies in my first walkthrough of KH when I was 13 and I did get the chests in Hollow Bastion, so there's a way, we just have to figure it out or remember how we did it. I'm about done with Neverland, so once I get to that part, I'll try to follow my old guide book and see if I can get them. If I can't... well then we have an impossible glitch in our hands.
Edit: So I finished Hollow Bastion. There was nothing in the Waterway. I found the same chests that were in the guide book, just different items. I got all the puppies too, you just have to search around. If the old game guide said that was a gummi there, there's a high chance that it's puppies instead. I found one of the puppies in the great hall and in an secluded area in the lift stop.
I found this, if you click on the tab for Final Mix, you can see where the puppies are now. The one that I think some are missing is the Lift Stop one. I didn't even know about it, I just did it by accident. All you do is when you are trying to get to chapel to get Maleficent, there is a switch near the great chest, what it does, it moves this huge contraption, that changes the direction of the lift in the library. All you do is do that, go the library, get on the lift and it will take you to that area, where the chest is suspended in the air. Just use Gravita and open. :3