He didn't want his troops to be using them because he wanted them to be reliant on the fact that medicine may very well run out and they should be able to take care of themselves without chems to heal themselves. But Caesar isn't a foot soldier that is meant to be in the front lines of battle, this rule doesn't apply to him but it does not make him hypocritical. The idea behind it is the same as with guns or why he doesn't want the Legion to be using robots to fight wars. Because what if they run out of it? What if they lose their gun in the battle? What happens when a soldier becomes naked in front of their enemy. Caesar wanted his soldiers to be able to adapt to any situation and so in regards to medicine he instead allows them to create their own herbal medicine that they can easily craft from resources they can gather themselves whereas chems would need a lab to be created. And like I said, he's not a soldier. He's a leader. The rules of the soldiers does not apply to the rules of the leaders. He's no more hypocritical than any other leader of any other faction. So you wanna call Caesar a hypocrite? Ok, call all other leaders that get special perks because of their position hypocrites as well. Does it ultimately matter if he's a hypocrite when everyone else is too?
It's not too much different from an officer giving strict punishments for her soldiers drinking alcohol while they are employed by the army but drinks some alcohol herself when at an officers party/gala/whatever. The soldiers minds needs to be clean and alert as they are in the field where they could be attacked by hostiles. Hers does not when in a special circumstance, such as a party where the point is to build ties with other officers and to let all the higher ups get to know one another so that it'll be easier to communicate with one another or be able to come to certain deals or share ideas. She does not have the same job as they do. She does not have the same kind of responsibility that they do. She has other responsibilities and so long as she can do them it doesn't matter if she can blow off steam every once in a while. She earned that right by becoming an officer in the first place. She gets special privilege, sure, but she also has greater responsibilities.
If she's a hypocrite then so is Caesar, but so is anyone remotely equivalent to them.
As cold hearted as it sounds, it does not matter much if a soldier dies from lack of chemical meds, but an entire nation can feel the impact if its leader dies, especially in a time of great strain.