MEAN Project - Organization
I don't see much difference as well. It should actually be driven by the team. Your code organization could be beneficial if you had a separate front-end and back-end teams. I've seen an environment when UI guys only downloaded UI portion and hooked up to REST back-end deployed somewhere on DEV server.
Number 2 is release procedure. If your front-end and back-end are tightly coupled they will be released together for 99%. Then you don't need to handle 2 repos. However if your back-end will serve as REST service end-point for other clients, not only your UI and you plan to release front-end changes without touching the back-end (no downtime for external clients) you may want to use two separate repos.
Also think about your CI server. You may want to run front-end an back-end builds and tests separately. However for most CI servers it does not matter either it is one repo or two.