In the Blade films why is EDTA able to destroy La Magra but has no effect on Reapers or Jared Nomak?
That's because Eli Damaskinos, the creator of the reapers, genetically engineered them to be superior to vampires in every way. One of his focuses was the removal of all the weaknesses common vampires had.
It is never stated how exactly he removed/reduced each weakness (that would slow the pace of the movie down). (Perhaps a bone case around the heart, faster infection rate thanks to a barbed tongue, immunity to Silver and Garlic and increased resistance towards EDTA making it only stun/hurt them instead of killing them).
The explanation to how he was able to counter EDTA is that the events of Blade 2 take place two years after the first movie in which EDTA was used to pretty much kill a vampiric god. Knowing that such a weapon exists, Damaskinos would have made it a priority to counter it in his next generation of vampires. Admittedly two years is a short amount of time for such a mutation to occur, but Damaskinos did have a large pool of resources to work with including vampire scientists who required much less downtime than a human one would, and of course a long series of test subjects they just nabbed off the streets. The short duration they had to perfect their new breed might even be the reason why it still affects them to some degree.
That was quite literally the point of the 'Reapers', genetically modified vampires without the weaknesses of normal vampires, created by splicing altered vampire DNA with Blade's own highly resistant 'daywalker' DNA
That being said, given the novelty of Blade's EDTA weapons, presumably resistance to it was a coincidence rather than something that was being intentionally aimed for.
BLADE: Keep talking, Stevens. Tell me why.
STEVENS: (sputtering). The Shadow Cabinet. For decades they've been trying to find a way to rid themselves of their hereditary weaknesses. Viral epidemiology, immunochemistry. Recombinant DNA was the next logical step.
NYSSA: (genuinely horrified). No, that's not possible. They wouldn't keep something like this from me...
Your father didn't want you to know. (haltingly) Something went wrong. The Reaper strain was too aggressive. Then Nomak escaped.