Encryption will slow things down somewhat, but I don't have any figures (as all NIH systems are required to use encrypted drives).
You can speed things up at the cost of using more disk space by setting various environment variables (e.g., in your .afnirc or .cshrc files)
AFNI_COMPRESSOR to NONE
AFNI_AUTOGZIP to NO
These will prevent AFNI from compressing output datasets, which will be faster both on output and on input.