ditto everything polarbear said.
The significance of fluency scores is that they provide a bit of quantitative information on how much effort/time he has to put into work, mainly at the basic skill level, in order to achieve the high-level results of which he is capable. In the case of reading comprehension and written expression, fluency challenges (possibly among other things, such as expressive/receptive language) may actually be preventing him from demonstrating higher level skills. At this level, he is probably recruiting cognition to compensate for the lack of automaticity (most notably in mathematics), which allows him to generate pretty high-quality work, especially with unlimited time. As academic demands increase, if these basic skill weaknesses are not remediated, they will progressively become greater and greater obstacles to success on higher-level reasoning/problem-solving/application tasks, because he will be devoting a great deal of mental processing power to skills that other students will use negligible energy on. This can be extremely frustrating, as one ends up using a lot of work, with little to show for it.
So the fluency deficits are not necessarily only about speed, but about efficiency.