As with all posts and topics on the web for X vs Y the choice is decided by how fit for purpose X or Y is for the job. It's the same for the case of the shotgun microphones both long and short.
A shotgun microphone is a microphone with an interference tube on the front. The tube with the slits in the sides. Now a long shotgun has a longer interference tube than a short shotgun. This is because long shotguns are for picking up sounds that are further away. This is not by amplifying the distant sound but by cutting the off axis sounds via the longer interference tube.
This has its benefits and drawbacks. Major benefit is the ability to exclude a lot of exterior noise from the source. Very handy for filming a period drama where a motorway can be heard (in the distance, this won't solve all your problems! Shotgun mics short and long don't reject low bass frequencies as well as they do mid and high frequencies) A criticism is the loss of natural quality from the sound source this is because of the loss of exterior background reflections of the source.
The short shotgun has less of a benefit and less of a drawback in those cases. The shorter interference tube combined with the lobular pickup pattern provides more directionality than a hypercardioid. The short shotgun is a very popular all round mic with the most notable being the sennheiser 416. Even though its been around since the late 70's.
To conclude: its good to have a shotgun in your arsenal of mics if your out in the field. For most situations the short shotgun will do for 97% of scenarios where you need directivity from exterior noise. The long shotgun has its place mainly in sports and environments where you need directionality over everything else.
Hope this article helps. Feel free to share and like this post or leave a comment.