Most of the fungi and bacteria and for that matter protozoans that you will find living on and in old woood will not be pathogenic. The small number of pathogens living in that environment will be vastly outnumbered by beneficial bacteria, fungi and protozoans.
Of course, they will be breaking down the wood and creating new soil for you plants to grow in. So, the relative chances of your plants acquiring a disease from composting organisms is pretty low.
Basically, what I am saying is that unless the wood has been treated with some sort of toxic compound or painted with a lead based paint, you shouldn't need to worry about cleaning them.
Just make sure that you don't use a sterilized soil when potting up your plants and add some non sterilized compost to the mix.
With the soil organisms that will already be in and on the wood, you will have a great soil community and your plants will be healthy and grow vigorously because of this with less chance of disease.
Disease usually occurs when we do all this cleaning and stripping of flora and fauna because we wash away and kill all the beneficial organisms that keep the pathogens at bay.
I will also provide this advice:
Spray your plants with a foliar spray of aerated compost tea (that you can brew at home if you like) to provide the foliage with a healthy population of flora and fauna.