I've arrived at the craters for two frezarite meteors that have fallen on sand, only to find a total of two blocks of frezarite between them (including those melted into water). Initially, I thought this might just be a temperature problem, but later I also found a large kreknorite meteor crater (it had spawned the portal) which was completely empty.

This is very odd. I ran a few tests myself and all the meteors' blocks had spawned just fine. I even tested it when a meteor is spawned in an un-loaded chunk.

A question I have just for clarity is are you sure these weren't just comets? Comets won't leave any damaged blocks behind so there shouldn't be a crater, but there could only be 1-4 blocks of ore.

Hmm, no, these were large craters, two covered in ice and one on fire with a nether portal structure hovering above (though I did find several normal meteors in the same desert and they seemed fine). Unfortunately I can't provide pictures as I was playing with the ImpactFlux pack and died. I guess it could just be bad luck? Will test when I have some time at my computer next.