Joe-
To answer some of your questions...
This exact document was discussed (briefly) on the Soviet Awards Forum. You can follow the link on Sebastien's post to the thread. This document is located on the third page.
Even not having seen that (as I didn't when I did the first part of my post) I still am suspicious of it. The reasons are several:
-The brown "tinting" on the inside of the document pages. This coloration has plagued other fake documents discussed on both forums. Realistically, I'm not sure how a document would have the pages turn this shade of brown without some application of some sort of agent that would turn it that color. I've owned probably 500 wartime Soviet IDs and other document books since starting collecting Soviet militaria in 1992, and can't think of any that I've owned that has had the inside paper turn this color.
-The solid black ink. In those same documents that I've owned, I can only remember a handful with still-solid colored black ink. And that ink was almost a "paint" consistency applied with a metal nibbed pen (leaving squared edges). This ink was applied with a pen - a different type of application. Also note that, even though the paper shows wear and discoloration, the ink is still very black with no fading or damage equal to the amount of the paper.
A note on the quality of Soviet documents: Yes, there was a variance of quality between some organizations in the Soviet system. Documents to a member of the Supreme Soviet are of very high quality, whereas documents for a field NKVD officer often depended upon the quality of materials available to the local command making the document (which included captured materials at times!) However, most documents were of similar quality, and since this document appears to have been issued by a front command, I wouldn't expect it to be of equivelant quality to that of a Supreme Soviet document, but at the same time, I think Smersh was pretty well funded AND their documents were a VERY important part of their job (often their only means of identification when in plain clothes) which would point in the direction that their documents were of above-average quality.
-The letters for numbers. I'm not saying that this is a "show stopper", but it says "No" and then is immediately followed by cyrillic "BD". I don't know if perhaps there was supposed to be a stamped serial number following the BD, but that's a little odd, especially if it's missing when there's a plethora of stamps and other writing in the document.
-Another thing that's not a show stopper but is kind of curious is the uniform on the colonel. This picture was supposedly taken in December 1944. At that point in time, very few people had their "defense" medals awarded to them, which calls into question his six ribbon bar rack. I can see a Red Banner for the top award, followed by a Red Star, then probably followed by a For Military Merit ribbon (and that's assuming that he got ALL his long-service awards at one time and assuming that he was a Civil War veteran with continuous service) his second row of three would have his XX Years ribbon and then... What other two? Potentially he COULD have gotten either of the ones for Moscow, Stalingrad or the Caucuses, but having them all by December 1944 would have been impressive (not impossible, but impressive). What I'm hinting here is that my hunch is that the picture probably dates from the immediate post-war period - a bit newer than the document's dates. However, this is just a hunch - there is a possibility that he very well could have had legitimately six ribbons by December 44, but that would be impressive. ALSO, another item to note... My listing of awards for him is assuming that he's a long serving officer. A good number of Smersh officers were brought in as "direct assessions" from the civilian world. I had a very nice award group to a civilian political functionary that was brought directly into Smersh as a Lieutenant Colonel straight from civilian life.
-I'd like to see the stamps up close as well. Once again, it's not impossible, but I've seen very few documents with excessive stamps, which this one has. For some reason, the Soviets were fond of only stamping what was needed - thus calling into question two stamps on the photo. Why would they need that?
My only real concerns regarding it's originality are the top couple reasons - the tinted paper and the black ink. The others are conjectures of things that are a bit out of place for most Soviet documents from the same time period.
Regarding the disposition of the documents after Smersh closed down, or after the person left Smersh... As I recall, Smersh was pretty much assessed into the KGB. Thus, the "retired" documents suffered the same fate as most KGB documents - taken after the person left the service and put into the departmental archive. These documents held a LOT of weight in the USSR, and they were very careful about how many were out "floating around". I've owned a half-dozen Smersh award groups, and despite how much extra paper that was included with the group, I never got any of the ID booklets. (Perhaps all my contacts were selling them on the side!)

Now, where did the booklets on the market come from? After the fall of the USSR, a number of archives were opened and their contents released to the collecting world, thus making them available on the market in the former USSR for a short time back in the 90's before they dried up and virtually dissapeared.
As far as the wear on the document because of the owner, I'd say that would be a fairly small factor. This document would have been carried on a regular basis, so I'd expect some wear to it. Also, the insides normally fade no matter who the owner was - just look at the older general officer ID documents - they tend to show realistic fading and wear even though most of them date from the 1960's.
I read the initial description for this document from eBay. As an editorial aside, Smersh was actually a small unit that acted in more of an "internal affairs" role rather than what was indicated in the description. In the example of my civilian-turned-Smersh guy, he was the senior Smersh officer with a staff of less than a dozen attached to an entire Corps! Hardly the guys that would be tasked with shooting retreating troops! None of the gentlemen (and one lady) whose groups I owned changed their names or did anything out of the ordinary from their veteran peers. In fact, that's one other suggestion... Smersh documentation was Army (or Navy or Air Force) property, and Smersh officer's service records (and citations) are kept in the Russian Ministry of Defense archives. You might try your luck at researching this guy by name and seeing if you can find a service history on him (which often have photos in the case of the more senior officers). Just a thought...
Anyway, hope that answers your questions!
--Dave