Oh yeah there are actually 3 encounters that are impossible to get because they forgot to put them in the game: the Dark Troll, Emerald Fire Crab and Doxy Queen
I think other than that everything is in the game? HP1GBC has 1 card combo missing but I don't think it's not the case in this game
I do agree not getting all the items feels a bit strange but it's always hard to come up with a proper definition for 100% and I feel like items that you can technically get as many times as you want and that get erased on the beginning of a new playthrough (which we need for 100% since you can't get all cards in 1 playthrough) is bit odd to require for speedruns, a lot of the items from sidequest can also be sold in the shop which I think is also strange if you were to require an item that you can just sell in the shop so I personally like our definition more but I totally understand what you mean :D