First, your realtor is working for you. Tell him what you require in a home, which includes the ability to have a smallflock (give him the minimum of what is acceptable: if you really want a rooster, tell him that the property needs to allow it. If you want 25 hens, don;t settle for property that allows only 3. This is no different than telling him that you want at least 5 bedrooms, a finished basement, a three car garage or any other feature that is important to you.
If he/he is not willing to find property that meets your needs, look for another realtor--and let him/her know that that is in the forecast if you do not get the information you want.
Next, re you talking about deed restrictions of HOA covenants. They are not the same thing. HOA covenants are not in the deed. That it is a part of an HOA probably is, but not the specific covenants. Many states require that HOA covenants be recorded documents. Any time you look at a property, you need to specifically ask if it is part of an HOA, and if so, ask to see the covenants. You also need to ask if there are deed restrictions, and what they are.