we almost agree, but not.
functionless proteins? yes , I guess it could be (but protein killers like ubiquitin will trash most of them)- but, be carful not to mix "functionless" with "useless".
and I will explain:
even a "usless protein", one that has no catalitic function, has an effect, how so?
it may bond to other cellular components, or aggragate in the cell (usually it is bad news for the cell), or change the osmotic tension by its sear existance.
you see, no free meals and easy answers in biology.
there are no inert proteins.
they all count.

about the other part, i must compleatly disagree.
unless we are talking about a strees enviroment, exposure to hunger (and so on), I believe the body (or selection, if you want) will NOT minimize the energy loss of these "functionless proteins"
we are very enrgy wasting.
that is the fundemental differance between a human made machine and a nature made machine- nature, unlike us, does leave loose-ends in it's creations

at last, we agree!
it will be reasonable to essume there are redundent copies of a gene.
in fact, we know there are, the phenomenon of redundancy of genes, and of metabolic pathays is well documented.
also, the existance of pseudo-genes (mentioned in this talk many times) is a indirect proof for such redundencies ,
as they used to be genes, but the body tolerated their loss of function (because they had doubles).
another point to take in mind is the regulation of expression, mainly feedback-inhibition, which means the more protein is created, the less it will further be created.
in this kind of regulation, the original amount of proteins will stay the same even if the body will make duplicates of the gene.

if I may diagnose you for a second,
your problem is not with the lack of knoladge, but in your rigid concepts, which you continiusly stick to : good-mutatuions, bad-mutations, ussless-proteins, and so on.
these are all simplifications, the data we knowy shows us that they are all ralative and not constants..