Any mod or saved game from the original version should still work with the GOG version. Depending on the type of mod, you may need to do a little tinkering.

The directory structure and file names are almost identical to the DOS version (with some additional files and folders from DOSBox and plug-ins for the GOG Galaxy client). Although the SAVES folder for your saved games is now named "cloud_saves". Even if you're not using GOG's cloud-save functionality, that's where all your saved games go. So if your mod is a simple save-game file, just drop it into that cloud_saves folder then load it up in-game.

If the mod actually modifies or replaces the game files, then you may need to do a little more tinkering. WAR.EXE is the game's main executable file. So if a mod uses a different .EXE to start the game, you should rename the original WAR.EXE to something else then rename the mod's new executable to WAR.EXE. This will preserve all the GOG shortcuts and DOSBox configurations which allow the game to start under Windows. Using a different executable to start the game may also cause your saved games to go back into the SAVES directory.

But, in theory, any original mods should still work.