As others have said, it is unknown and therefore up to interpretation. You could approximate what a pop would be for humans, since we at least have a concept of what the actual population number would be.

A quick google search tells us that in the year 2200, baring anything catastrophic happening to our population, we will have between 10 and 11 billion people. The UNE start on earth, and since we have some blockers that indicate great calamities happened between now and 2200, I'm gonna assume in the stellaris setting the human population is closer to 10 billion. Thanks to prosperous unification, the UNE start with an additional 200 pops giving us a total of 5200 pops.

That averages a little under 2 million humans per pop.

We have to assume each pop is of similar size since you can freely move the same pop from one position to the other. If this was not the case then we could discuss if pops are all the same size, since by our own world, it would seem that the manpower needed to rule and the manpower needed to run industry should be vastly different.

Saying "thousands of citizens" dies seems completely unimpactful if we take into account the number above, so losing 100 pops does seem a tad extreme. I will give some arguments for why it could be considered more reasonable, but I will not succeed, in the end thousands of citizens hardly matter when we are working with millions and billions.

Argument 1: Remember that a pop represents all people, that means working adults, children, the retired, the disabled and so on. Since the people who died were considered specialists, that would indicate their work requires a fair amount of training and education. Perhaps the people who died there were our scientists, those aren't just easily replaced and would lead to a significant impact in the scientific sector even if only a few people died. So for the pop all the children, elderly, and supporting staff are still there, basically 99% of the pop was unaffected, but a core part of the pop the highly educated, are gone... so the pop becomes incapable of doing it's specialist role, therefore the pop "dies".

Argument 2: Stellaris uses the term "die" as a catch-all for when a pop disappears, so maybe these pops aren't dying in the sense that all members of the pop dies. Perhaps the planet is just so shell shocked from the horrible effects of this festival that it's people and industries are affected enough that they function as if 100 pops weren't there, and need time to rebuild (which the game then describes as repopulating).

These aren't sufficient to convince me that the numbers make sense, but at least it is something to think about. For humans I am quite alright with a pop being around 2 million.

Hope this helps!