Total speculation... but maybe because C git clone always reads from local disk (?). jgit clone appears to read from Bigtable/GFS, and those systems have in-memory caches, or columns can reside totally in memory. Also you could probably make use of parallelism in I/O with cluster of servers, where as with local disk you are probably limited by there being a single disk head that has to move around.

So I doubt it has anything to with Java, but the underlying storage. If I'm wrong I'd also like to hear about it!