Andy,
Mainly, the tubes where you are putting the Cat6 cables shouldn´t be a problem at all. There are some considerations about Cat5 and Cat6 cables, HOWEVER, i sincerely don´t think that it should be something you are planning to take care.
Look, usually Cat5e should have as better quality issues and performance of cat6 to most applications. If you are looking for 1 GB networks, which most of new NICs are intended to be used, AND if you are talking about home networks, keep your money and use cat5e. Don´t hesistate at all.
Cat6 are mainly used for higher speeds and higher needs. In fact, I did a consultancy to a Brazilian datacenter which uses cat6, and they said that their needs could be achieved with cat5e, but regarding international standards and other things they decided to use cat6.
Everything on cat6 are expensivier than cat5. I personally use cat5e at home and office and can handle GB speeds with no problem.
Lets go back to your old pipes. Regardless of where you are, there are some international standards with obligates the installer to have all water plumbing really grounded. I don´t think that you may experience any problems. Before doing anything, make sure you don´t have any voltage running on this pipes. Could harm you. Old installations may have problems, but this shouldn´t be your problem.
Remember only to find out where this plumbing are running, since you may encounter some interference IF this pipes run real close to some lightings.
Anyway, I can tell you that you may use either cat5 or 6 with that tubing. Remember: no water inside the tubes.
REGARDING FIHART ANSWER:
We can say that the quality are just as good. Indeed it has nothing to do with quality itself. The cables are completely different. Different wire sizes, different reinforcement, cat6 has an internal "septo" which leads all 4 pairs totally separetad and OF COURSE, you can´t plug or insert a cat6 cable into a cat5 connector. Why: it does not fit! The RJ45 connection for routers, switchs and other stuff are the same, but the other part of the connector are not the same. Nor the prices!
Keep your cat5e and enjoy a dinner with friends with the rest of your money.
Hope this help.
LUIS