The only difference is that the device won't appear as a disk on your computer with MTP. Garmin's update software won't care, and Basecamp can use MTP devices which will allow you to send/receive data from your Nuvi. But Mapsource is older and will not be able to communicate with the Nuvi in MTP mode because it won't see a mass storage device to read/write its files.
You also won't be able to backup your nuvi by copying files to your computer in MTP mode. I guess Garmin is using this now in order to prevent users from messing things up on the device by accidentally deleting files or reformatting (plenty of threads here where that has happened). Aside from that, I can't see any reason not to use mass storage mode. But if you don't want to backup your Nuvi and don't need to use Mapsource (or other older software) to transfer data, it really won't matter.