Nutanix uses the VAAI (vStorage API for Array Integration) plugin to allow for quick cloning of VMs. This allows the cloning to be offloaded to Nutanix for a faster process. VAAI can't be used when a snapshot is present on the VM which explains the difference you are seeing.
I am using Horizon View so this clone activity is delaying the Recompose task and Shadow clones are enabled. Is there anything specific I can change or suggest the customer ?It takes approx 5 minutes for 30 GB parent machine with 2 GB of Snaphots max
I would suggest reading the best practice guide http://download.nutanix.com/solutionsDocs/RA-2058-VMware-Horizon.pdf. In Support I've specifically seen slowness and errors when host caching/ storage accelerator is enabled on View. I would check to make sure it is disabled. If it is I would advise opening a case to have a SRE investigate further.