Raman, The age you are at now, its unfortunate for you what the destiny made you witness ! You need not to know why grown up persons indulge in these things, what makes them do it, whether it has began with reluctance and forced/ blackmailed or done with consent or what!
You may not understand or would not believe that even some husbands makes their wives to sleep with boss or some other influencial person for financial or official gains like promotion or raise or for getting perques in the job! I am not saying that your father made her sleep with his boss. I am just pointing out the probability. If you check the older questions on this site you would find a question by woman who slept with the boss of her husband for promotion of her husband and he came back to her asking for more and requesting to make it a permnant arrangement for forever. So it may be possible that she might have made a sacrifice for him (your father) and boss would have came back asked more and she consented .
Now the deed is done and can not be erased And unfortunately for you , you know what you should have never known.
Look have a liberal attitude. Its very clear from your narration that she was enjoying the act when you saw them . So under whatever circumstances she was doing it or had done it , it was always necessarily consensual act.
When two elders do something like sex with consent and if it is not hurting anyone physically and they are not breaking any law or committing a crime then in my opinion it is not a big deal and i agree morally it is a crime and if really your father is innocent and after knowing this he may leve her and in the process you would suffer the most.
So in a subtle way make your mom aware that you know what has been going around when only she is at home. You can tell her that neighborhood friends of your teasing him that in the ansence of you and your father some one suspious visits house and remains inside in the house. Grab the picture of the parked car outside your house with a cellphone and show her the date and timings and ask an explanation. If she opens up then you would know how and why it started in first place. May be possible also that your father would not be adequate in the bedroom so she might have adopted relation with this guy or simply he would have been paying her money , costly gifts etc. Anything is possible. But remain calm. Keep your eyes open and see if you have any unexplained new things in her wordrobe, expensive jewellery , expensive items in your household. Avoid telling your father right now. First give her an opportunity to come out of this and most important thing is have broad and liberal view on the things. Best of luck ! Do keep us informed!