In a lot of Semitic languages, including, to my understanding, Hebrew, you can add the corresponding pronoun between a noun and adjective to clarify that you mean the bird IS pretty. Some linguists even say pronouns are starting to get re-analyzed as copulas in certain dialects (like Egyptian Arabic). I'm not sure how formal or correct it sounds to a native speaker, but it's pretty neat.
I agree with you that ציפור יפה tsipor yafa only makes sense as pretty bird or a pretty bird or a beautiful bird.
However, if you try to translate ציפור יפה as “a bird is pretty”, Duolingo will mark you wrong, because for that sentence, Duo requires Ha-tsipor hi yafa.
I can't say for Hebrew. But in Arabic you would not phrase it this way. You would naturally say: The bird is beautiful. The bird has feathers... - Languages function differently at times. We can't always literally translate. We have to go a step further and learn how a native would express himself.