It's pretty obvious that the TOS stardates have to roll over to zero once per decade: they covered about 5,000 stardates during the five-year mission, so 0000.0 to 9999.9 would take a decade. Just like in TNG.
It's just that TNG marks the decade with an extra digit; the TOS heroes may simply have dropped that digit because they knew very well which decade they were having their five-year mission on. (The TNG folks with their "ongoing" mission only drop the century digit, because they still very well know the century they live in!) STD could make this explicit, using four-digit stardates but mentioning what the fifth digit for their decade is supposed to be.
if STD is going to jump from era to era, it might well cover several stardate systems, with the heroes commenting on that. It's not as if one would make more or less sense than the other.
Timo Saloniemi