From what I gathered there should be a homeworld 2 exe but apparently it appears absent from this version? I want to play the homefront and warlord mods but I don't know what to do. I'm worried I might've made a mistake getting the gog version.

You can find the homeworld2.exe in your %InstallDir%/Homeworld2Classic/Bin/Release directory.

I'm not sure if mods are officially supported for the GOG remastered version but I think at least mods for the classic versions should work.

In case of the warlord mod, putting the files in the Homeworld2Classic/Data directory and using the launch parameters specified in the readme seems to work fine, haven't tested other mods so far (aside from the Trail engine fix)