How can I copy directories recursively with hardlinks with variables in bash?

Yes, you can accomplish this task in bash by using the rsync command instead of cp and modifying your find command to use variables. Here is an example command that should work for your needs:

#!/bin/bash
# Set source and destination directories
src_dir="Dir1"
dest_dir="Dir2"

# Use find to locate all files in source directory with only one link
find "$src_dir" -type f -links 1 | while read file; do
  # Get the directory name of the file and create the corresponding directory in the destination
  dir=$(dirname "$file")
  mkdir -p "$dest_dir/$dir"

  # Copy the file using rsync with the -l (hardlink) option
  rsync -av --link-dest="$src_dir" "$file" "$dest_dir/$file"
done

You could do that with tools like find, and mkdir

In a bash file .sh dont forget to replace /path/to/Dir1 with the source directory path and /path/to/Dir2 with the destination directory path.

#!/bin/bash

src_dir="/path/to/Dir1"
dest_dir="/path/to/Dir2"

find "$src_dir" -type d -print0 | while IFS= read -r -d '' dir; do
    dest_subdir="${dir/$src_dir/$dest_dir}"
    
    mkdir -p "$dest_subdir"
    
    find "$dir" -maxdepth 1 -type f -links 1 -print0 | while IFS= read -r -d '' file; do
        cp -al "$file" "$dest_subdir"
    done
done