Would I be disadvantaged in PhD admission if I took only few courses each semester during my Bachelors and Master’s?
During my undergrad I took 3 courses because: 1. I was working part time 2. My doctor recommended me to take a reduced course load. For my master’s program, I was working full time for my parents’ business. I didn’t mention this in my PhD application, which i think I should have. But it is too late now, the deadline has already passed.


Those sound like perfectly good reasons for a reduced study load to me, and yes, you probably should have at least mentioned your concurrent employment.  Since you were working concurrently with your studies, you might also consider adding that as a standard part of your CV (i.e., in the employment section), which would mean you would not need to make special mention of it in future applications.

Admissions for PhD programs are generally made based on assessments of the quality of applications by academics, and they have wide discretion over what they consider to be relevant.  Opinions on the relevance or non-relevance of a reduced study load will differ among different people, but I suspect that most academics will be interested in your mastery of the undergraduate material ---as reflected in your GPA and other relevant outputs--- than in how long it took you to attain this mastery.  There is no definitive answer as to whether this will affect your application, because it will be assessed by people, and people do all sorts of different things.

Achieving a 4.0 GPA while working concurrently in various jobs (and full-time during your Masters) is a crazy-good record, so you should definitely have mentioned your employment.  Even without that your academic record sounds very strong.  Nevertheless, if you are worried that you have an unexplained gap in your application, it might be worth sending an email to the admissions office giving them a short supplementary paragraph explaining that you undertook your studies at a reduced load because you were concurrently working at such-and-such hours.  (I would suggest you not mention your medical issues, since this would raise more questions than it answers, and your full-time work is already an adequate reason for a reduced study load.)  Ask them if they could please pass this supplementary information on the assessors of your application.  Even though the applications deadline has closed, you might find that they are willing to pass on a short supplementary paragraph; but keep it really short.