Not every bug you find requires treatment in the first place. Many that are considered to be harmful forms are actually normal flora within limits. Many species are found in the intestinal tract of every snake in small numbers. As long as the immune system is keeping those numbers in check, they cause no problems and do not require treatment. Those include, but are not limited to E.coli, Entamoeba ssp., and certain Coccidians, even Cryptosporidium serpentis. The decision to treat is based on:
1) Numbers (per field) as compared to normal load
2) Clinical symptoms presented
3) General condition of the animal
4) Special considerations regarding species and indicated drugs.
Even in the case of Nematode, Cestode, Pentastome or Trematode parasites, certain levels may be acceptable and not require treatment. All of the drugs used to treat these bugs carry some level of risk to the animal. If the risk of the parasite infestation is less than the risk of the medication, then a decision not to treat would be appropriate. In some cases, depending on the general condition of the animal, even if there is a heavy parasite load present, treatment may not be possible. In severely dehydrated animals, many of the meds used carry a significant risk of nephrotoxicity. In that case, supportive therapy would be needed to improve the condition of the animal before drug therapy could be used.