An interesting question. Never really thought about how few might still be in existence.
Disclaimer: I'm not a statistician, but found this to be an interesting little exercise.
A quick search suggested this would not be easy to estimate. U.S. loss statistics that I found were often monetary. Theft statistics are particularly difficult to integrate, because the insurance industry reports a theft recovery rate approximately 95% of "value." I don't know to what they are referring when they say "value." Is it replacement value, book value, insured value, 95% cars recoverd (doubtful). I did find some statistics that extrapolated U.S. numbers from hard data that had been gathered in Canada. These estimates suggested a rate of 4% per year vehicles "totaled." The numbers were generated from statistics dating back 20+ years as of 2002.
I assumed a similar rate of loss for the MKIV during the production run (93-98), thinking that MKIV's were NOT driven as collectibles/Sunday drivers at that time. Even if this were not entirely true, I figure any reduction in percentage loss due to less frequent driving might be offset by the insurance industry's predicted increased rate of loss due to the sporting nature of the car.
By my calculations a rate of 4% per year would leave 3411 6MT MKIVs at the conclusion of the 1998 production run. This seems like a large number of MKIVs lost, but consider that the comparable loss to the Ford Taurus pool over the same time frame would be approximately 90,000.
I then assumed a decrease rate of loss by a factor of 10 from the end of production in the U.S. to the present, presuming that many MKIVs were treated like collectables in the post production years. This would predict 3276 6MT MKIVs remaining today.
Anyone in possession of more relavent statistics, a more accurate application of the data than I have listed above, or issues with my assumptions please chime in.