That's an astute observation, jake, but somewhat dated... In fact the term "C-Value paradox" is undergoing evolution (no pun intended) or more accurately a metamorphosis, in it's application, definition and even the term itself.
Richard Sternberg and James A. Shapiro wrote recently that "one day, we will think of what used to be called 'junk DNA' as a critical component of truly 'expert' cellular control regimes" ("How Repeated Retroelements format genome function," Cytogenetic and Genome Research 110:108�116 [2005]).
In article (actually a thesis) entitiled "Evolutionary Computation and the C-value Paradox", biologist Sean Luke, of George Mason University explains "...why do some �complex� organisms have few genes while
some �simple� organisms have many?" ... (from a footnote) "...As the C-value Paradox is not a �paradox� any more per se, Gregory has suggested using the term C-value Enigma instead.
Since then some junk DNA has been found to serve one
purpose or another in the genome, so at least part of it may
not be junk after all. At any rate, the term �junk� is falling
out of favor..."
Finally, from a thesis authored by Margaret Beaton and Thomas Cavalier-Smith, published by the Royal Society states "... Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA...", "...The skeletal DNA theory explains why nuclear genome size increases with cell volume and, using new evidence on nucleomorph gene functions, why nucleomorph genomes do not"...