Snapshot not showing up in snapshot manager doesn't mean VM is not running on snapshot.
cat VM_name.vmx | grep -i vmdk
See if you see any file with VM_name-00000x.vmdk, if yes consolidate it.
IF not, then you need to look into other factors like storage performance etc
Orphaned delta files can cause serious performance issues. These files still remains after the snapshot deleted/removed. These are also represented by Zombie Files. You need to use the PowerCLI script to get the list of Orphaned VMDKs. You can cross check and then try deleting them.
Refer Below Link:
I have also used this script in my past experience, you can test and then try using this.
If VM is not running on snapshot and have orphaned delta files. It will not cause performance issues as they in no way contribute to VM's running process or any process will not access it untill you run another snapshot.