Well, the 100% stat doesn't mean
much by itself either. We should expect the government to be bringing cases with fairly solid proof for starters, so 100% is nearly indistinguishable from the ideal scenario.
But more importantly if the judge indicates they won't sign it without changes, then the changes get made and it ends up eventually counting as a signed warrant.
If the judge says they won't sign that warrant at all then the government withdraws it before formally filing it; again, keeping the stat near 100%.
In fact the only warrants by these metrics that wouldn't end up signed are the ones that the government felt so sure about that they didn't even bother vetting it with the judge first before formally submitting it, and the judge had to actually reject it.
With all that said, I do agree that this standard of oversight is severely lacking compared to the capabilities of the NSA. Allowing companies to give stats regarding NSLs and other warrants is only the tip of the iceberg of improvements that are needed to transparency, oversight, and accountability; not just with PRISM, and not just with NSA.