Why not? Not only was he young but he would have never seen Tobi in akatsuki, only Pein. 'Tobi' wasn't apart of Akatsuki during that time as he only surfaced in Part 2 of the Series as Deidara's partner which would explain why Itachi had to search him out. Deidara Joined Akatsuki without seeing Tobi, and Tobi himself said that he first met itachi when he searched him out. It may be a timeline error but a connection can be made.
Lots of problems with your assumption there. For starters, Deidara joined Akatsuki quite late compared to Itachi, when it was first formed Tobi was the de facto head who introduced members who joined. One proof of this is Kisame's first joining. Another major flaw is the timeline. Over
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when Obito first only
just met Nagato, there's less than a year left to the kyuubi attack. The uchiha massacre takes place 6 years after the kyuubi incident. At the time, Nagato did'nt even start using Pain's corpses, he had'nt even joined Akatsuki. For him to become the de facto head of that organization and develop his pain identity in such a short time is highly improbable, if not impossible. As you can see
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the hidden rain was ambushed by remnants of the former regime a 'little while ago' to part 2. Part 2, which was 10 years after the uchiha massacre. Before he even established himself completely in the hidden rain, doubt tobi would hand over akatsuki's leadership to him.
But that's still speculative. The ultimate proof, as i already pointed out to you is Tobi meeting itachi and not knowing him(he would've if he had already joined akatsuki) and hiruzen's statement.