Both files are used as input files for your GPSr to create the actual file (.gpi) that the unit uses for your custom pois. They can be used interchangeably with POI Loader to create this file.
The advantage of the .csv file is it's simplicity (view and edit in Excel or any text editor). The advantage of the .gpx file is additional information and functionality. For example, if you have a GPSr with bluetooth functionality you can enter phone numbers which can be dialed from the GPSr when selecting the POI.
The .csv files are smaller, but that only affects the storage on your PC. For the same information, the resultant file created on your GPSr through POI Loader should be the same.
My suggestion to you is to do a search on this website for .csv and also for .gpx where you will find much more detailed information.
- Garmin CSV file format
- Garmin Custom POIs | nuvi GPX / CSV display differences
- POI Files | How do I create a GPX File?