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If you're thinking about encrypting your whole drive with LUKS at install time than none of these concerns pose problem. I am encrypting whole disk on my laptop for obvious reasons (if I loose it or it gets stolen) and haven't noticed any performance hits or problems.

  • Only thing that is different is that while booting it is prompting me for LUKS password and boot takes 5-10 seconds more than usual (last boot it took 6 seconds more by looking at systemd-analyze blame).
  • Since you're decrypting your drive at boot time there are no differences for applications since they interact with files as usual.
  • Copying from and to encrypted drive is basically also the same since you decrypt it while mounting.

I hope that answers all of your questions :-)