Well, I'll start with a full disclosure: I only grow from seed (at least so far), so I am by no means an expert on cloning...
Having said that, clones from a 2 year old plant, are 2 years old also in a certain biological sense - and age does make a difference in some respects. (To really blow your mind, a clone of a clone is also still the age of the original mother).
I don't believe that it makes you more prone to hermie issues, though (maybe someone else can weigh in on that). I know some growers have mentioned they feel vigor decreases with age and will "bud out" their mothers yearly, for example, to keep from progressively weaker plants/yields. In theory, the loss in vigor could result in susceptibility to disease, and plant health problems (again not sure if that would increase likelihood of a stress hermie - but it might stand to reason).
Clones don't have quite the yield potential as growing from seed, and their yield potential goes decreases over time as I understand it. But, it's a great way to grow in that clones of a female, are going to be female, etc., and it's much cheaper than buying seeds.
My guess is that your plants would have been fine, though, if your environment was all in check. You have wisely identified several potential causes for stress that could have made this happen on almost any plant -- the key is to make a few adjustments to insure an even better outcome in the future. You are learning a lot and doing great - it's a process and you'll keep getting better at it all the time.