As said below, the sequence of the junk DNA does seem to mutate a lot faster than parts of the DNA which is known not to be junk, heavily suggesting that at least the exact sequence is not so important.
Furthermore, in rats and mice, large swaths of junk DNA have been experimentally removed, without any detectable effect on the phenotype.
If the junk DNA has any positive effect, it may be to protect against viruses or transposons inserting themselves into random areas of the genome. Keeping the majority of DNA "useless" may decrease the risk that these insert themselves into vital parts of the DNA.
Furthermore, in rats and mice, large swaths of junk DNA have been experimentally removed, without any detectable effect on the phenotype.
If the junk DNA has any positive effect, it may be to protect against viruses or transposons inserting themselves into random areas of the genome. Keeping the majority of DNA "useless" may decrease the risk that these insert themselves into vital parts of the DNA.