That's not a significant enough difference that I would conclude there's any effect. A better "profile" is:
#!/bin/bash
echo example.sh
/usr/bin/time sh -c 'for i in $(seq 1 1000); do ./example.sh; done'
echo example.sh.bin
/usr/bin/time sh -c 'for i in $(seq 1 1000); do ./example.sh.bin; done'
On my machine, I got:
example.sh
39.46user 33.22system 1:16.92elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+8547221minor)pagefaults 0swaps
example.sh.bin
42.33user 42.13system 1:33.98elapsed 89%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+9376313minor)pagefaults 0swaps
That is not enough to show definitively that the "encrypted" one is slower (though I obviously think it is), but it certainly shows that the encrypted doesn't consistently take less user time in a simple benchmark.
Also, there are some other serious issues with your code. Most obviously, this isn't close to sound encryption. As other people said, you're approaching the problem wrong. A encryption algorithm you come up with "in a matter of hours" is not a substitute for sound permissions.
Further, you need to use makefiles instead of proliferating unnecessary shell scripts. Learn rudimentary gcc options, like -o. Don't attempt to copy to /usr/bin/ unless the user runs an install target (in which case /usr/local/bin would still be better).