Jousting roots - a matter of skewering carefully?

[Phyrex]

In order to check the moisture of all my plants I use the widely recommended method of sticking in a skewer and checking how wet it is when it's pulled out. It works perfectly, however, I do wonder about the following. How often do I joust one of the roots that I don't see when I'm trying to manouver around a piece of bark or a S/H pebble?? I really worry about doing that and giving the plant an infection of some sort? Is this really an issue or do I not joust any roots (usually)??