I couldn't agree more. Many knock-out mice for protein coding genes don't have an "obvious phenotype", but they are conserved across species. When studied in detail they often reveal an effect, be it in the response to environmental stress or subtle behavioural alterations.
I can't find an updated reference, but results published in 2012 by the Mouse Genetics Project and the International Mouse Phenotyping Consortium indicate that ~20% of coding gene knock-out lines examined don't have an "obvious phenotype" [1]. The most likely explanation for their conservation is that they do have a function and a phenotype: we just don't know what to look for.
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463797/