There is a very clear difference between "junk" DNA and "non-junk" DNA, the latter encodes proteins. That doesn't mean that the DNA parts that don't encode proteins are junk, this is more of an exaggeration or misunderstanding that is often repeated, but not what scientists thought.

There are clearly parts of DNA that are not essential, this is clear if you compare genome sizes between different organism. They can vary enormously, and not in a way correlated with any complexity of the organism. There are also parts of DNA that are remnants of viruses inserting many copies of their DNA, which are the parts that could be considered junk. Even those might have an effect simply due to their presence, but essentially everything in the cell has some effects if you look closely enough.