Yes, I've seen ones in the zoo.
is simply wrong. This response should not be used. The word "one" is not used in the plural in this construction.
One might say any of:
- I've seen several in the zoo.
- I've seen some in the zoo.
- I've seen them in the zoo.
- I've seen koalas in the zoo.
I would favor the first two myself, but any of these or of several possible similar responses would be perfectly acceptable.
A comment asks if one could reply with:
Yes, I have seen it.
No. First of all "it" would indicate a specific animal, previously referred to or identified, as in:
A: Have you sen the koala that the zoo just got?
B" Yes, I have seen it.
Here a specific koala is in question.
Also, some people object to using "it" for living beings, even ones that are not human.