This is quickly going to devolve into pedantics. If junk DNA refers to sequences with no function (as opposed to sequences with no known function), then there won’t be discovered any pieces of junk DNA with a function even in the future.
Of course this all depends on whether we know with certainty which sequences are in fact junk DNA(not functional) or not.
Since we do not, yes it is likely true that there will be a few more things presently thought to likely be junk DNA, that will be discovered to be functional in the future.
But honestly, so what? Genetics and molecular biology is a scientific field, and the idea that we can label and define ourselves out of the predicament that laypeople can become confused out of ignorance (or being misled by propagandists) seems to me utopian in the extreme.
So what is the alternative? Suppose we change the label to just “functionless DNA”, we are still left with the question “which parts are we certain have no function?”, and so there will just ALWAYS be a space for propagandists to say “see the evolutionists used to classify this as likely being functionless, and we are discovering more and more function among the functionless DNA”.
Changing the label does nothing for us. It’s junk DNA, just call it that.