@Hexparrot has put in limiters on spesific folders to make sure MineOS ignores the folders having the highest number of files, but yes, MineOS may bog down due to number of tiles in a server directory:
var default_skips = ['world', 'world_the_end', 'world_nether', 'dynmap', 'plugins', 'web', 'region', 'playerdata', 'stats', 'data'];
(from: https://github.com/hexparrot/mineos-node/blob/master/server.js )
So as far as I know, MineOS should ignore any dir known to contain huge amounts of files. Of course, using a custom world name, may force MineOS to look inside a folder anyway, but even inside the “world” directories there are dir that are skipped by default (region and player).
HexParrot can probably better answer what mecanisms used to prevet MIneOS from hanging on reading through loads of files.
As for the minecraft server itself (the java part) it is handled throug the linux service “Screen”, so each server is run an contained separately as distinct proscesses…