As far as harmful to the ants? Naw, nothing beats good ol rain water but if you think about it, we drink the tap water, we give it to our dog's cat's other pets, out kids, of course we adjust it but we use it to fill out fish tanks, we water our plants with it etc.......
As far as hard water and stains, it really depends on where you live and how they treat the water. if your really worried about it go to your local Walmart (not sure what the equivalent would be over seas) and by some thing like a britta water filter attachment for your sink or a britta water pitcher that has the replaceable filter built in.
As far as mold on cotton and other things that are soaked that's because you contaminated the material in one way or another. If you want make sure you use gloves when handling the cotton and avoid placing it on a surface that might be unclean. You have no clue the amount of stuff that settles on a flat surface in a few minutes even if you think it's clean.
Clean your test tubes and then wipe them out with isopropyl alcohol. let dry upside down and then cap them until your ready to use them. that one way (I do that) to make sure your tubes stay clean until you need them. Don't place them in a dish washer and use the dish washer detergent that you use to clean your dishes, many of those have a lot of additives including bleach and such that might be left behind when they dry.
Ok enough ramblings form me.