There's a crappy script system that you really do stuff with, and yes it's pretty clear mods are an important part of the game, at least for servers. You need loving DLLs or SOs (Linux) to make mods for the game. Worthless.
By the "script system" are you referring to configuration files? I think those were only meant for automation. Most of the server mods are just to make dedicated server administration easier, and many features used in these mods have been added to the vanilla game (map voting, team scrambling, etc). I don't think modding was really supposed to be a big part of TF2, so the developers never really bothered with an easier modding system.