water has minerals in it....
Unless you are boiling it in a completely sterile pan and with distilled water, chances are you are doing more harm than good. Tap water has many microscopic minerals and other hard elements in it; depending on your water source you may have more or less of this (hard or soft water)
Have you ever boiled water and noticed that white ring in your pan? Or Noticed a residue on the insides of your dishwasher/pipes after a long time without cleaning?
Those are hard minerals and other microscopic particles in your water. Almost everyone has them, some less noticeable again depending on how hard or soft your water is.
When you boil cotton, all you are doing is introducing these hard elements into your cotton and while I doubt its harmful to you, it will most certainly make for cotton that does not soak up juice as well, nor taste as good.
This goes for any wicking material, anytime you boil these things you are introducing minerals into the wicking.
Actually most sterile cotton is sterilized using autoclave, which is a wax...waxes are insoluble in water so boiling isn't likely to remove much wax.