The metabolic energy cost of manufacturing them. If most of your DNA is "filler" what is the selective advantage of excessive spreading of functionless replicators? You need to explain how such DNA arose in the first place and why it is not speedily eliminated, since it contributes little or nothing to the fitness of the organism.
Cordially,
Conservatively, I estimate you probably have to use two molecules of glucose to provide the energy and materials to make one nucleotide and insert it into DNA. The L-GLO pseudogene has about 1000 base pairs, or 2000 nucleotides. If there's one copy in every one of the 5 X 1013 cells of the body, to produce two L-GLO pseudogenes in every cell of the body, you need 2 X 2 X 2000 X 5 X 1013 = 4 X 1017molecules of glucose, or about 7 X 10 -7 moles. The molecular mass of glucose is 180 g/mol, so this corresponds to approximately 125 micrograms of glucose. So a human possessing the L-GLO pseudogene needs to eat 125 micrograms more glucose to synthesize all the L-GLO pseudogenes every cell in the body will ever have. Turnover times for human DNA vary from days to decades, depending on which cells we're discussing; but if we take a mean of 100 days, you require 1.25 micrograms of extra glucose a day to maintain the L-GLO pseudogene.
And that assumes degraded DNA is not recycled, which of course it is.