I don't think he anticipated De-Fusion, but he did anticipate that Yugi had that Spell Textbook planted along with the Spellbinding Circle earlier in the duel. If adding those 500 ATK points to the 3400 Paladin would have from one dragon being on the field still makes it significantly weaker than BEUD, Kaiba would just not use Absorb Spell since it's not worth trading off another card. Kaiba's used plenty of cards that put the opponents cards on the field to the graveyard or make them discard from their decks, he might change his strategy if Dark Paladin poses zero threat even with its 500 ATK boost from BEUD's presence. Kaiba said that he observed all of Yugi's duels from the past, so he knows Yugi has stuff like Mirror Force in store, he even summoned Mirror Force Dragon in the Doma filler. It's perfectly reasonable to think that Kaiba might prepare for Yugi having face down traps, especially since Fake Kaiba used a counter to Mirror Force with Negate Attack before.
Also, Yugi only activated De-Fusion after Kaiba used Double Spell, expecting a spell counter card like De-Spell or Magic Jammer. If he knew Kaiba didn't have a counter to non-equip spells he'd just have used De-Fusion right away, and then strengthened Paladin further with Spell Textbook, giving it 5400 ATK. Meaning that Yugi definitely anticipated a counter to the first spell he'd use, and only used De-Fusion once he realized Kaiba was out of face-down cards. If Kaiba knows Dark Paladin is only 3900 ATK even with the equip spell, then he has little reason to fear the equip spell so he might use something else as Yugi feared.
