Be careful around cat feces if you are pregnant it harbours toxoplasmosis and is airborne and will harm your baby do not handle cat litter if you are pregnant. However, you do not need to worry about that if your cat is an indoors-only cat, as toxoplasmosis is extremely, extremely rare among indoors-only cats.
Animal urine is not hazardous to your health. I have both cats and dogs and have never had any health concerns caused by their urine.
If the room has urine everywhere, the ammonia may be an irritant, but there would have to be a lot of urine! As a lifelong pet owner, I personally never have had any problems.
I have two dogs and they have had "mistakes" when puppies. I spot clean and then I spray vinegar on the spot which dilutes the odor and the dog WILL NOT piddle there again. I've had no problems.
I have two large Labs, They occasionally go indoors, NOT my fault. I clean but the air is full of the heavy odor. We have never had any throat problems in our home. Lately everyone of us has had bad throat problems. I am talking about a family of 5. I can only hope this is not caused by the dog urine but I have no other explanation.
Get videos or find a trainer to teach your dogs not to urinate in the house. Try using a solution of vinegar and warm water and spraying it quite heavily. This will get to the rubber under-padding of the carpet (where all pet stains end up) and the vinegar will dilute the urine smell. If it's too bad you may have to rip the carpet up and put Pergo flooring down if you can't train your dogs to ask out or at least have a newspaper someone down the hall by the laundry room where they can go if it's an emergency. I own 2 dogs and a cat and they've had the odd mistake (even vomiting) but have never had any smells in my house by using the vinegar. As far as sore throats, look towards the real culprit ... sprays! Often people don't realize how often they may spray their carpets, countertops or clean the air with sprays. Too many sprays can cause sore throats.
With Urine there's always a risk of ammonia irritation, which can cause eye irritation and a variety of respiratory problems, and if inadvertently combined with chlorine during cleaning could (possibly) create trace amounts of chlorine gas (which is extremely poisonous).
With the feces, you should manage it, regularly clean up after your pets and dispose of the feces outside of your home. Particularly when dealing with a litter box in a closed space over long periods of time, there is always a risk of Hydrogen Sulfide poisoning, so litter boxes should be cleaned regularly. Early signs of hydrogen sulfide poisoning include eye irritation, sore throat and sinus irritation, sudden bursts of sneezing may occur. If the problem escalates it may cause temporary loss of voice/raspy voice, and may also cause nausea and vomiting, but these are all also common symptoms of communicable illnesses. Normally pet owners would not allow the problem to escalate before cleaning their litter box, but people have before, particularly people who lack their sense of smell.
