We are installing a new toilet and discovered that condensation had left the subfloor dark with water damage. We have sprayed the area several times with Black mold killer, but are wondering if there is more that we should be doing.
Is this enough to eliminate the mold on such a porous material as wood?

How do we prevent condensation from creating a problem again? It is a copper pipe coming up through a rough drilled hole in the floor with a shut off valve at the top. (fairly standard)

Any advice would be appreciated.

condensation had left the subfloor dark with water damage
Yes, constant water will darken wood. And yes, if water is present long enough mold will grow. Mold spores are every where. They are part of the natural process of decay. But what makes you think it is Black mold? There is a difference between mold and Black mold which is toxic to humans. Either way, a little diluted bleach will kill the mold spores.
The only way to prevent new mold from growing is to remove the water source, which is or was most likely a leaking valve or connection. Not likely to be humidity.

I don't quite get all the fear of mold. Most of it is not going to hurt you, no matter how black it is. I've lived surrounded by it for years. Many people get sinus congestion and a few people get more complicated respiratory problems. I just use bleach on all mold, and a scrub brush. A toilet bowl brush works too. Ventilate the room while using straight bleach and don't ever mix it with any other product. Let the area dry for days.

http://www.quackwatch.com/01QuackeryRelatedTopics/toxicmold.html
No need to read all of it to get the drift.