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mkdir -p /boo /boo/dir1 /boo/dir2 /doo/dir1 /doo/dir2 /foo /foo/dir1 /foo/dir2
touch /boo/boo_file /boo/dir1/file1 /boo/dir2/file1 /doo/dir1/file1 /doo/dir2/file1 /doo/doo_file /foo/dir1/file1...

No need to mkdir -p /foo if you already mkdir -p /foo/dir1 as the -p option creates parents.

#!/bin/bash
for d1 in boo doo foo; do
for d2 in dir1 dir2; do
mkdir -p /$d1/$d2
...

-p is required, yes, or I wouldn't have put it there.

if you already have a file named 'boo', it will fail. delete it.

It fails because you are trying to create those in `/' and you are not root.
Remove the `/' in front of directories in the script