Just me but seems to me you are probably over thinking it. I don't know if the S indicator is a new thing in Austin or not. If it's not, it sounds like not all DMV employees are aware of that requirement to add onto the license thus why some deaf don't have it on their license.
I wouldn't care- it may in fact be a positive aid when/if I got stopped in letting the police know to be aware. AND in fact if there is a problem and they 'claim' to not have known of my deafness, can point to the license and say well it's right there in black and white.
Texas isn't the only place- there's a few other states who have similar restrictions-
Illinois is Type F-
http://www.ilga.gov/commission/jcar/admincode/092/092010300000920R.html
In Missouri it is J88 though there you can ask to have it added (or not)
http://dor.mo.gov/pdf/Chapter1.pdf (page 10)
West Virginia has a lil symbol for deaf that can be added at request
http://www.transportation.wv.gov/dmv/Manuals/Documents/Manuals/2013-Drivers-Handbook.pdf
Trying to find info on Texas but in a hurry.
If judging by other states in that drivers can ask or omit the indicator, it sounds like whoever you met with in the DMV either had no clue what they were talking about or took the guidelines as a firm "Yes you MUST have it on there" rule.
I disagree with "it's not that common for people to be deaf"- there are all kinds of people who fall under that term.
The wording of the regulations may be outdated (with the exception of antique cars- there's still a lot of those out there), I don't see anything wrong with some sort of indication.
I wouldn't be outraged but if concerned then yes send feedback to the DMV and indicate where you went. Maybe they'll be nice and re issue your license...