My wife puts lemon in her drinks, including water, all the time (men don't bother with such frivolity) and she never gets sick. My understanding is that most bacteria (type and concentration) that live on the outside of food is easily killed in the digestive process and if not, you get a free cleansing.
Do you wash your hands between peeling and eating an orange? Do you wash the orange before you peel it?, No? You know your contaminating the flesh of that orange with the bacteria you picked up off the peel..tsk, tsk. We know all the people involved in the process of delivering that orange washed their hands regularly so don't worry. LOL
So the bottom line is, if you're the kind of guy that likes lemon in his water (and then worries about it), foodborne bacteria is not your biggest concern (hair care products probably are).