He may very well have suspected this truth, but couldn't have known for sure. Unless maybe John told him so before he went back in time, of course. I don't remember if there's any canon one way or another on that particular point, and I haven't been keeping up with the more recent movies in the franchise.
The events of the first Terminator movie take place over the course of a few days, at most. Sarah herself didn't even know she was pregnant until it was all over. For all Reese knew, Sarah could already have been pregnant before he arrived (and not yet aware of it), or she could have become pregnant by another man later (after his death, once he knew that was coming.) So, even knowing John's age in the future is not conclusive proof that he was the father.
Even knowing John's exact birth date wouldn't be enough to deduce this information conclusively, since the human gestation cycle is not 100% predictable and every woman's pregnancy is unique. A baby is considered to be "full term" (ie: not premature) if it is born after 37 weeks, but it could be as many as 40 - 42 weeks before medical professionals decide to induce labour artificially (depending on a variety of factors.) There's basically a whole month of potential wiggle room there.