Really? Because Itachi used four.
1. Amaterasu
2. Tsukiyomi
3. Susano'o
4. He used a weakened Kagutsuchi when he put out the Amaterasu on Sasuke's body.
It's likely that Itachi unknowingly used a weakened version of Kagutsuchi, the same way Obito unknowingly used Kamui to slip into Madara's hideout. The difference is, Itachi never became fully conscious to the ability of Kagutsuchi, especially because he used his Mangekyo far less than Sasuke.
We've seen Mangekyo users have just one, or two abilities. Shisui had one ability, KA, while Obito had two, two variants of Kamui. The number doesn't have to be three, and Itachi has shown.
Now, let's look at Sasuke having Tsukiyomi or not. Sasuke has shown to use a Genjutsu from his Mangekyo on Killer Bee. This Mangekyo is the opposite one to Amaterasu, and it had the same reverse color scaling as Tsukiyomi. When Sasuke used his Genjutsu against Danzo, Danzo specifically compared it to Tsukiyomi. Tsukiyomi isn't a technique Itachi uses often, and Itachi is a genjutsu master, meaning he has many more up his sleeve. Why would Danzo compare Sasuke's genjutsu to Tsukiyomi in particular when Itachi has many other more well-known jutsu? In fact, if we look deeper, why would Danzo compare it specifically to Tsukiyomi's ability to manipulate the perception of time, if Sasuke hadn't used Tsukiyomi. If someone throws a rock at you, would you say the rock is useless, and then stress this by citing the sharpness of a knife? No, when comparing two things, they have to have a similar aspect. Danzo's comparison was that Sasuke's jutsu lacked the ability to manipulate perception of time, and Tsukiyomi is the only Genjutsu known to be able to do such a thing, so obviously, Danzo was saying Sasuke had a weaker Tsukiyomi. All you need is the basic ability to put context clues together.