Well, the MUL has them available to ComStar through the centuries. Basically, IMO, ComStar can justifiably have anything that the Star League produced, just not necessarily many of them. The same with the Clans really. Though most of the Clans probably wouldn't be using them.
So yeah. The Clans and ComStar could've easily had access to them.
I'd also point out that extinct doesn't necessarily mean completely gone, just "not really enough to be worth mentioning." IIRC
Comstar could have found some sitting around, but how likely would one of the best assault mechs available at the time would have been left behind? Those would likely be the first to be loaded up, each one of them accounted for, before anything else was on those dropships. I'd say that there is less then a 1% chance that there were any left behind. Id bet that there would be a pile of SL lights sitting around for every thunderhawk loaded up.
The clans would likely make use of them as second line mechs. Of course this ignores that FASA was shoveling "old" mechs into the then current time line. Anything could be suggested considering what was left behind by the SL. Also, the clans and Comstar could have produced any number of thunderhawks and mothballed them. It changes how the story would have gone, instead of an Orion and an Atlas kicking in the door it would have been an Orion and a Thunderhawk at the very least.
What it really boils down to is that nobody outside of comstar and the clans would have had the information and facilities to produce a thunderhawk. Any existing mechs were either destroyed, taken with the traitor, or lost to time and sitting in a forgotten facility on a forgotten world of the I.S. making the mech effectively extinct to the I.S.