There are several things to keep in mind.
- According to Harry Potter and the Chamber of Secrets, the cry of a mandrake is only fatal if the mandrake is fully grown. A juvenile mandrake would knock anyone who heard it unconscious for several hours, but its cry would not kill them. Given that the purpose of the battle was to delay (not defeat) Voldemort and the Death Eaters, juvenile mandrakes could have helped to buy time. The books do not clearly state that the mandrakes had reached full killing potential. They were probably not young juvenile plants, but we do not know how large they were, or whether all of them were at the same level of maturity.
- There were a lot of Death Eaters. We only know the important ones by name. The fact that none of the Death Eaters we know were stunned or killed by the mandrakes' cries, does not mean that no Death Eaters were affected.
- Chamber of Secrets indicates that the school was not in the habit of keeping a large supply of mandrakes. If there are roughly eight people carrying the mandrakes, which are described as "large" and "potted," they probably could not have carried more than one at a time--two at the most. That means there were probably somewhere from eight to sixteen mandrake plants--not a huge number. As a result, there may not have been enough to throw over all parts of the castle walls. The mandrakes might have made a difference at a crucial section of the Hogwarts defenses, but there would not have been enough mandrakes to throw at all of the Death Eaters.
- For the mandrakes to take effect, they had to be heard--and battles are noisy. There would be yelling, of course--not all wizards are proficient at nonverbal spells, and not all wands will perform them (dogwood wands are known for having this problem). Any spells that missed there targets could hit parts of the castle or other physical objects, which would cause additional loud noises. The Death Eaters had also brought along nonhuman allies: the giants, in particular, were known for their loudness. Even if the mandrakes were full grown--which is far from certain--they would not have killed anyone if the battle noise drowned out the screaming mandrakes.
We do not know the extent to which the mandrakes were effective. What we do know is that Neville and the others succeeded in delaying the Death Eaters--and the book does seem to hint that the mandrakes had a part in that achievement.