You can easily diff the output of commands instead of files. In this case hexdump prints thousands of lines, but I’m only interested in the difference:

# diff <(hexdump file1.bin) <(hexdump file2.bin)
1,2c1,2
< 0000000 6a49 b610 0000 0000 5733 7261 4465 4243
< 0000010 0000 0000 0001 0000 9006 4e0b 0b28 000f
---
> 0000000 6a49 b616 0000 0000 5733 7261 4465 4243
> 0000010 0000 0000 0001 0000 9006 4e11 0b28 000f

Run the hexdump in subshell using parenthesis, then redirect the output back to diff. I’m only interested in the 2 pieces that are different for each binary file:

# for i in `ls *.bin | sort -nk1.7`; do echo -n "$i: "; hexdump -C $i | grep '33 57 61 72 65 44\|4e 28 0b 0f 00' | awk '{if(NR==1) print $4;if(NR==2) print $12}' | paste - -; done | column -t 2>/dev/null
file0.bin:   1a  15
file1.bin:   19  14
file2.bin:   18  13
file3.bin:   17  12
file4.bin:   16  11
file5.bin:   15  10
file6.bin:   14  0f
file8.bin:   12  0d
file9.bin:   11  0c
file10.bin:  10  0b
file12.bin:  0e  09
file13.bin:  0d  08
file14.bin:  0f  0a
file15.bin:  0b  06
file16.bin:  0a  05
file17.bin:  09  04
file18.bin:  08  03
file19.bin:  07  02
file20.bin:  06  01
file21.bin:  05  00
file22.bin:  0c  07