I would only say Y-E-S, and have only seen Y-E-S, as there is the lexicalized version, for clarification of the sign yes, (i.e. with a beginning signer) or if for some reason discussing the English word yes in a deep linguistics discussion about word meaning, (i.e. me signing to a Deaf person: the English word Y-E-S is not equivalent to sign YES or fingerspelling Y-S in meaning because...)
Basically, I would only spell Y-E-S, and have only seen it spelled, when talking about the English word yes. (It could maybe, possibly, RARELY be used otherwise, but it would be a one time event and not be repeated)
Also, the lexicalized version-- as all lexicalized signs are-- doesn't have the same movement as our usual "borrowing English words" fingerspelling. The Y to S does a little bit of a jump forward, and often has an upward swinging movement. -- Alas, I don't have a camera, but ask a fluent signer to show you this if you don't know what I mean.
Hope this helps!
(I'm a Linguistics major with a focus in ASL, can ya tell?)