A lot of it goes back to the Yugoslavian system, or to be more specific where the academies were located
In what is now Croatia there were academies in Zagreb, Split and Osijek, which Dinamo, Hajduk and Osijek reaping the benefits ever since, while what is now Serbia had academies in Belgrade and Novi Sad which Red Star, Partizan and Vojvodina are reaping the benefits of - which is why Kosovo is probably doomed to be spoken of alongside San Marino, as any of their best players were moved into the academies in what is now either Serbia or Bosnia
Similar can be said of the former Soviet Union, as there were prolific academy systems in Moscow, St Petersburg, Kyiv and Minsk (to name but four) which is why Russia and Ukraine continue to produce talent and Belarus isn't too shabby either, but the likes of Estonia, Latvia, Lithuania, Georgia etc etc etc don't have the infrastructure
it really sticks out when you look at the players some of those academies have produced
Dinamo Zagreb: Luka Modric, Zvonomir Boban, Robert Prosinecki, Mateo Kovacic, Niko Kranjcar, Milan Badelj, Vedran Corluka, Josko Gvardiol, Sime Vrsaljko, Dario Simic, Andrej Kramaric, Dejan Lovren, Igor Biscan
Hajduk Split: Alen Boksic, Igor Tudor, Stipe Pletikosa, Darijo Srna, Slaven Bilic, Milan Rapajic, Robert Jarni, Ivan Strinic, Nikola Vlasic
Osijek: Davor Suker, Donmagoj Vida, Robert Spehar, Jurica Vranjes, Nenad Bjelica, Borna Barisic