Personally, I go usually with a caching system within Drupal. How this is implemented really depends on the external system, and how it works, but essentially I'll pull the data from the external source when first requested, and save it within Drupal somehow, whether that be into a node, or a custom entity, or some other data entity unrelated to Drupal entities.
The reasoning behind this is that pulling data from a 3rd party application into Drupal, then delivering it to the user, adds a lot of overhead and processing time. Essentially the browser makes a request, Drupal then starts to build it, makes it's own request (same as a browser) to the 3rd party app, gets the data back, finishes the Drupal page build, and sends it to the browser. This can make for some particularly long page builds. Whereas, if you pull it the first time from the 3rd party app and cache it, it takes longer for that first request, but subsequent requests will already find the data within Drupal, making for faster page loads.
Some things to consider however:
- Will the data change every request? If so, then it should not be cached within Drupal.
- Will the data never change on any request? If so, then it should be created as either a Drupal entity, or a non-Drupal entity, within Drupal, permanently
- Will the data ever be deleted? If so, then it should be cached within Drupal, and periodically checked to see if it's been deleted. If however it must definitely not be accessed after it's been deleted, then it should not be cached within Drupal, else you risk showing the data to the user after it's been deleted.
- Can you cache the data safely for a period of time? For example, maybe you can make the Drupal cache expire periodically.
- Will you need the data to be accessible as fast as possible, when it's cached? You may want to create a cron mechanism that makes requests to the 3rd party for any new items, caching them immediately so they are ready right away when necessary.
Each 3rd party app is different, so there is not a one-size-fits-all solution to this. The various limitations and requirements need to be researched, with a solution created accordingly.