약 is medicine or medication. There is no difference. Medication should be accepted.
Is 약 the subject of the sentence, then? Because of the subject particle attached to it? Is this how all imperative sentences are structured, with the noun that the verb acts on being denoted with 는/은?
은/는 is the topic particle, not the subject one. So it's literally: "As for this medicine, take it every day." The speaker marks 약 as the central thing that they are talking about.
You can say '이 약을 매일 복용하세요' it's true you can say it like that. And also you can say '이 약은 매일 복용하세요' it's also a common expression. There is no need for use '은' instead of '을'. '복용하다' is a verb.