Due to fans wanting it and really loving it when they add a lot of them.
This lags the game so they can't go totally crazy without doing optimisations too and then it's a lot of work and something else may have to go (like supply and demand)
Florence is kind of a special case due to the fact that there were so many fans requesting it. Wiz even felt it was pointless. But again doing what the fans want is logical.
I am not entirely sure of your point, but adding ahistorical Sapmi seems pointless to me.
Re. optimization - cutting supply and demand, terrain% and whatever else was deleted is not optimization. Even recalculating trade (or performing other actions) only once per month is hardly "optimization".
Optimization is not synonym with "cutting out", it is about doing sth. better. If they made it so that dead AI do not perform any actions then number of dead AIs would not matter.
Obviously I have no idea what kind of data structure they use and what operations are performed, but also obviously in many places it is kind of list or array (from their comments on how things work - on many issues, when all other conditions are met, the "first country" is selected).
If it is a List then pruning it into two is trivial, if it is Array they should skip dead entries, and although length of loop will be still big, they wont do anything for most of. I am aware that saying it is much easier than doing, but if they wanted they could do it (and thinking about future DLCs and EU5 they will have to do it at some point anyway).