is it worth it to install SSD internally, instead of using USB3?
YES, it's definitely worth it. With my setup, sustained transfer speeds were roughly 75% better using SATA, vs. USB3.



I tested both configurations using ZoneBench as follows:

SSD: 120GB OWC Mercury Electra 6G 

Mac: Late 2012 Mac Mini, 2.6Ghz core i7, model ID Macmini6,2, 16GB RAM

Hot-Swap unit: StarTech USB3-to-SATA dock, model SATDOCK22U3S ver2

  All speeds are in MB/sec (mega-bytes per second)

  Configuration A: SSD connected via Hot-swap USB 3 Dock
  Lowest / Avg / Highest R/W speeds:  95 / 150 / 185

  Configuration B: SSD installed in internal HDD bay in 2012 Mini (direct SATA):
  Lowest / Avg / Highest R/W speeds: 145 / 250/ 460


All tests were repeated 5 times at intervals of 1 hour, under normal system usage. (A few apps open &amp; idle, CPU &amp; system I/O load 99% idle.)



As one can see, in this configuration, taking the trouble to mount the SDD in the Mini's internal SATA bay is well worth the massive performance gains.