"They are small animals."
Translation:To jsou malá zvířata.
This is the common "to jsou/jsou to" pattern. Please do also read other questions and answers here and under other sentences.
Oni jsou... is possible and accepted. But that would be most likely used if you wanted to say about a group of people that they are small animals. Quite weird but possible. But it could also be a group of animals if they are grammatically masculine animate. Anyway "to jsou" or "jsou to" is more natural here.
Nope, there is no agreement here, you always use "to" in "to je" and "to jsou". Consider "It is my mother." or "It is Jim." or "It is him.", no agreement either.
Is there a difference between "to jsou malá zvířata" And "jsou to malá zvířata?" I know both are correct but would you use one over the other in different situations or is one more common?
When you see some animals and you express your surprise or enjoyment you say more likely "To jsou...". If some animals were mentioned and you want to tell they are small you say more likely "Jsou to...".