I don't believe the veracrypt layer has anything whatsoever to do with the disk space issue. Veracrypt is a block layer that knows nothing about filesystems. Ext4 is a filesystem that sits on top of a block device. If you're not getting disk space back then it's a filesystem issue.

Considerations other than block size (discussed an in another answer) are sparse files and hard linked files being copied as separates. Both are managed by flags to `rsync`; both are ignored by your selection of flags. You can validate this by comparing the disk usage from these two commands:

 du -hsx /media/veracrypt1
 du -hsxl --apparent-size /media/veracrypt1

In your linked question you talk about backing up an entire system. In such cases you need to be careful to ignore memory-backed filesystems such as `/dev` and often `/tmp`. However, here you're using directory paths so I will continue to use those here 

 rsync -axHS /media/veracrypt1/ /media/veracrypt2

Notes:
1. The sparse flag will not replace existing files with sparse equivalents - you would need to process those yourself or delete them first.
2. Likewise `rsync` will not hard link files that are the same but not already hard linked; you would have to delete both beforehand.
3. Your original command would have created `/media/veracrypt2/veracrypt1`. By suffixing `/` to the source directory path you perform a copy directly to the destination without first creating a subdirectory named as the source.