I have little (or big) problem with one of my reference letter for Cambridge.
Today I get the sealed envelope from one of my referees... but when I get home and I "compared" it with the other one that I already had, I found that is lighter! Now, I suppose my second referee forget to enclose 3 copies of the letter...
The problem is that it is impossible for me to meet him again, because he was going to the US and he wont be back before the deadline.
Do you think it would be a problem for my application to be considered? Or they simply will make copies of the letter?

No, that`s not a problem, as the BGS will get copies for you if there was only one reference letter in the envelope.

Do you know if it is possible to send an additional reference letter? I have three years of work experience (5 including trainee program) but Cambridge requires "Academic References". I wish to send an additional reference from my employer. Should I just include it with the other references?

I'm sure that won't be a problem at all. I know someone who applied to the Yale JD program (different I know, but similar in the important ways) and sent 11 reference letters! I would definitely send an extra if you have it. Of course, I wouldn't send them purely for the sake of it (i.e. if you have 3 academic references I don't imagine a 4th will do much good, indeed it might diminish the impact of the others) but if you have one that is distinctive then sure, send it. Hope that helps!