Should I tell my instructor this?

Understanding why you were like that isn't the same as excusing it. Your instructor will likely still wonder why you didn't discuss this issue with him at the outset so the two of you could figure out appropriate accommodations together, or why you don't take the medication (or use other strategies for managing your ADD) during class when you know this is an issue.

If he's not your current instructor, and you're able to tell him what you've been doing since you took his class to fix the problem, then maybe he'll be able to work that into his reference. Otherwise, find someone who can give you a positive reference without hesitation, and if there's no professor who fits that description, then see if there's a TA or club advisor or some other option you can use. And be sure you figure out a better way to manage your work when you actually do find a job.

You won't get a more decent reference. When someone presents a reason for them not performing, it doesn't change their evaluation of you where they speculate on how good you could have been. All they have to go on is how you performed, your professor doesn't know how you would have done if you took your medication, and you don't know either so it's just not something he can comment on in his reference. No reason to tell him I think.

It's like when people talk about applying for college, and they talk about their lower GPA is because they had a really hard year (suppose a very valid set of events made it extremely difficult for this student to concentrate on their studies). Now, that explains it, but it doesn't excuse it and it doesn't permit you to be on the same level as others who did do well. Nobody knows how you can do in different situations, they can only comment on what you did do, and that's really the only way to be fair about it.

If you tell them you only take medication while you study, they may not be willing to give you a good reference because you could have taken your medication for when you are in lab as well. If you simply say you have ADD they will likely ask you if you take medication. I don't want to lecture you about there being no excuses because what's done is done. The best thing for you to do at this point is to find a different reference.

Ask a different instructor. Nobody in the workplace is going to cut you slack, ADD or not. Either you can do the job or you can't.

You should take your medication in lab, not just when you are studying.

Hell yeah i don't know why you haven't already told them. but do it honestly they should know