In my review of the Playstation 4 Pro, I spoke about periphals as well, including the USB3 external harddisc. I said that the speed of the internal harddisk was about on-par with the USB3 external harddisk. Now I can confirm this, but the external USB3 harddisk is a bit slower than the internal one though.

Yesterday my brother and I played Elder Scrolls online and we teamed up to do some quests together, which included a lot of going in and out of buildings and the Thieves guild. Those are the moments when the game loads it's assets from the harddisk. With my brother only using the internal harddisk and me having dropped ESO on the external one, the (slight) difference in speed became clear.
Where we both were about at the same time to exit an area (or to enter a new one - take your pick ), he was always a bit earlier in the game again then I was. The difference was about a second or so (and with ESO loading really a lot of assets for the world, it's almost nothing), there was a bit of a delay when loading from the external harddisk.

I also noticed this difference when playing Games of Thornes - a Tell Tale series (I'll give you my review on it later this month). I've bought the season pass disc with the first 5 games on the BluRay disc and the 6th one being downloaded. That download was stored on the external HDD automatically and when I reached the 6th season of the game, I noticed that the game was loading a bit slower compared to the load from the BluRay drive.

This means that (as I said), the external harddisk indeed is a bit slower than the internal one, and it's barely noticable. But when you're playing a game in multi-player mode, it advisable to have that game on the internal harddisk instead of the external one. Also, very small games (those under 3Gb, and most likely indie games) can be easily installed on the external harddisk. These games will load in one go and most likely have very little assets to load when switching maps/areas.