You're comparing KDB running on 4x Intel Xeon Phi 7210 CPUs, totaling 256 physical CPUs.
Compared to the best result for Java/Spark, which was running on 11x m3.xlarge instances on AWS. That's only 44 CPUs, plus it's running on AWS, not 100% dedicated hardware, so it's tough to tell what sort of an impact the virtualization + EBS has on performance. Plus, from the AWS page: "Each vCPU is a hyperthread of an Intel Xeon core except for T2 and m3.medium", which does not do anything good for the results.
Yes, technically, KDB was 199.80x faster (not 1000!) than Java/Spark, when it was given vastly superior, dedicated hardware without virtualization, and when tackling a problem that the hardware setup is optimized for. Note that the author calls this out by saying "This isn't dissimilar to using graphics cards" when talking about the setup he was using for the KDB benchmarks.
To get a sensible idea of the relative difference in performance, you would have to compare KDB and Java/Spark both running on the Xeon Phis, and/or running both on 11x m3.xlarge AWS instances - and even then, if Java/Spark does poorly on the Xeon Phi test, that might just mean that the Java/Spark developers haven't optimized for that particular setup.