The hdd is my comp's weakest part (the missions are loading a few minutes). So I thought the problem may be in the structure of the MODS folder created by JSGME and all these duplicated "Data" folders that hdd has to handle with. Probably that's why the game loads so slowly, reading hundreds of duplicated files. Unfortunately I don't have SSD drive which could resolve this issue.
Anyway thanks very much for the reply!

Greetings from Poland