I am not sure that I follow your question, but I think you are asking that if the dns server given to the AP and their clients is from the SRX are they independent from each other. The answer would be no. All the AP would be sharing the same DNS and all the cache and other behavior is based on all of their actions as a whole and not individually as units.
Still not sure I am getting your use case. Now you seem to be referencing the dyndns service so are you talking about having the APs register a dyndns name for each?
If that is the case they will all have the same ip address using default nat setups. If this is the problem you see with dyndns and you have other ip addresses in your carrier assigned pool you could create custom nat source rules to make sure each AP gets their own nat ip address.