Manually deleting Snapshot File from Datastore

Do not delete a snapshot file manually.
Only snapshot manager understands these files and has the functionality that will affect it. If you manually delete them then there will be no way to recover the data.

Since you are just wondering, NO, it won't work and its a good way of messing around with a machine which is running well.

Sometimes, VMs run on a snapshot , but the snapshot does not show up in the Snapshot Manager...

There is a KB Article which explains how to commit/delete them when they don't show up in snapshot manager.
Do not delete them manually at any cost
This is the KB that will help you with a situation when they don't show up in manager
http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1002310

That is correct, because the Backup Application has FAILED to remove the snapshot, and that's really as bug, but it's a very common issues.

see my EE Article

HOW TO: VMware Snapshots :- Be Patient

http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=2003638

I found this above article and Video..I thought it is related to what I am looking for

Consolidating Snapshots, a nice feature to have in ESXi 5.x, does not always work!

because the link below posted by Abhilash Hb, is not really clear the way they describe the Resolution:

http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1002310

How you resolve a snapshot issue, which does not appear, in Snapshot Manager, or refuses to consolidate is as follows:-

1. Take a Snapshot.
2. Wait 60 seconds.
3. Delete ALL the Snapshot in Snapshot Manager.

(done).

If that does not work, or Consolidate does not work, more work is required.

BUT, if you find yourself with A SNAPSHOT, and not sure how to handle or have the confidence to deal with it yourself, I would suggest posting here on EE, of support call to VMware.

Thank you