First, there’s really no trouble for me – taking it apart and putting it back together is quick and easy. While I was at it, I also replaced the thermal paste.
Second, yes, there’s no speed difference, because I’m using this Mac Mini as a network storage device, and the speed is limited by the 1 Gbps network card anyway.
Third, why would I want an external drive dangling on a cable outside the case, when I can have it neatly installed inside?
Now the additional external drive can be used for Time Machine backups instead.
And by the way, everywhere I looked people said it’s impossible to fit a 5 TB drive thicker than 7 mm in there. Well, I’ve proven it’s perfectly doable, and anyone who can take it apart and reassemble it can manage it.