"ler" is used when the subject is a human being. It's optional for human beings and forbidden for non-human stuff.
"Kuşlar neredeler?" would sound like you expect the birds to gather in a place, start discussing and making decisions and so on; you humanize them. It's something that you could see in faerie tales and children's stories.
It's a set of Turkish grammar rules you've been following all along without realizing there are formal rules for it. :)
Read this for a thourough explanation: https://turkishteatime.com/turkish-grammar-guide/vowel-harmony/
An excellent question but one which has been answered previously on this page. The simplest answer is that it's optional. However it is only optional when the verb is referring to humans. When the verb is referring to anything not human then the plural must not be used. So, in this phrase because the verb in Turkish is in the plural it is clear that the subject the verb is referring to is human. I hope that clarifies things for you. (Typing this has definitely clarified it my mind.)
Strictly speaking every letter in Turkish is pronounced. So ne-re-de is correct. However, as with Enlish (and I imagine with other languages) native speakers often take short-cuts. Until you're comfortable with your fluency and are regularly understood it is best to stick to the rules.
Ok, I know there are many explanations all over the place for the optional "ler" for humans ("Onlar neredeLER?") . I'm very sorry if I missed it somewhere, but will someone please give a clear, in-depth explanation as to WHY there is (what I call) subject-verb disagreement in Turkish? Why is "LER" omitted for all things that are not human? You have "Kuslar nerede?" and "Onlar neredeLER?" Why does this human/ non-human difference for "lar/ler" exist in Turkish? Thank you in advance for a patient, thorough answer. :-)