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I often wonder where the biological scientists get the idea that just because we don’t know what something is for, that it can only be junk.

The junk idea has nothing to do with science, and everything to do with evolutionary philosophy.

The meaning of the term "junk" in the phrase "junk DNA" is generally misunderstood, because it was a handy term for the popular press and other nonscientists to grab onto. But the guy who originally came up with the term in 1972 wrote, in his paper titled "So Much 'Junk' DNA In Our Genome" (note the quotes around "junk"--apparently he didn't mean it to be taken literally),

The creation of every new gene must have been accompanied by many other redundant copies joining the ranks of silent DNA base sequences, and these silent DNA base sequences may now be serving the useful but negative function of spacing those which have succeeded.

So from the beginning, "junk DNA" was thought to have at least a passive role. And in 1990, another scientist was being interviewed:

Kimura: I was very impressed with the statement that 98% of the human genome is junk rather than garbage. Our daily experience suggests that sometimes 'junk' is valuable. Is it possible that some of the so-called junk genes might be found to be valuable...?
...
Brenner: ....In one sense, organisms are very much like us! You get a wooden box and decide to keep it to make a bookcase out of it one day, but you never do because it's much cheaper to buy a bookcase, and so the wooden box remains as junk....
...
Davis: Is it possible that some, or much, of the as definable a function as, say, making an enzyme, but has regulatory roles that will turn out to be more than junk?
Brenner: I would be a fool if I denied that; it is possible, but that is another question I am going to leave for our successors. I am certainly not going to try to prove or disprove it for every piece of junk, and I shall avoid it.

So the idea that biologists were convinced that "junk DNA" had no purpose whatsoever was never really true and certainly hasn't been true for nearly 20 years, despite the efforts of some to make it appear that scientists are being blindsided by these discoveries. As someone pointed out, there's a reason they're investigating the stuff in the first place.