It really depends on the source. If they are trustworthy and known throughout the community for the app in question then probably yes and you should research what others have to say about the mod (forums etc, assuming they are there. discussed), but otherwise it's a real gamble especially if you're just looking for cracked / licensed versions of paid apps (a very common way for bad guys to trick users into infecting themselves with horses of Troy and others).
Honestly, the only thing that is 100% sure would be to only use unmodified apps from official sources, or if there are official modified versions (as is the case with some games, for example, especially when 'they were published as open source), to download them.
The type of app you're trying to download can also play a big role in this, as some apps are more likely to be targeted by malicious actors than others. For example, pirated paid software as I mentioned before is a common target, as are many games, especially those launched through Steam, as many threats seek to collect Steam login information and game assets that have value (such as in-game items that they can sell for real money).